Differential accessibility analysis of toxoplasma infection in human

Loading libraries

library(DESeq2)

## Warning: package 'S4Vectors' was built under R version 4.1.3

library(vsn)
library(affy)
library(ggplot2)
library(ggrepel)
library(ggbio)
library(factoextra)
library(FactoMineR)
library(reshape2)
library(biomaRt)
library(EnhancedVolcano)
library(viridis)
library(ComplexHeatmap)
library(clusterProfiler)
library(enrichplot)
library(org.Hs.eg.db)
library(pheatmap)
library(tracktables)
library(dplyr)
library(plyr)
library(ChIPpeakAnno)
library(ChIPseeker)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(GenomicFeatures)
library(GenomicRanges)
library(rtracklayer)
library(GenomicDistributions)

colors <- viridis(6)[c(1, 6)]

Loading ATAC-Seq quantification

# read in RangedSummarizedExperiment
cnts <- readRDS("/Volumes/GoogleDrive/My Drive/Greally_Lab/Toxoplasma/Human/ATAC-Seq/Quantification/Non-redundent_narrowPeak_optimal.rds")
rownames(cnts) <- rowData(cnts)$symbol

sampleTable <- data.frame(condition = factor(c(rep("Infected",
    3), rep("Uninfected", 3))), row.names = colnames(cnts))

dds <- DESeqDataSetFromMatrix(countData = assay(cnts), colData = sampleTable,
    design = ~condition, rowRanges = rowRanges(cnts))
# set control
dds$condition <- relevel(dds$condition, ref = "Uninfected")

Pre-processing

Unnormalized count distribution

• No filtering required as distribution shows minimal low values

# total counts
barplot(colSums(counts(dds)), horiz = TRUE, col = colors[colData(dds)$condition],
    las = 1, xlab = "Counts", main = "Total Counts")
legend("topright", legend = levels(colData(dds)$condition), lwd = 1,
    col = colors)

# Unique regions
barplot(colSums(counts(dds) > 0), horiz = TRUE, col = colors[colData(dds)$condition],
    las = 1, xlab = "Unique Regions", main = "Regions detected")
legend("topright", legend = levels(colData(dds)$condition), lwd = 1,
    col = colors)

# plotting an unnormalized density plot of the log
# transformed counts
plotDensity(log2(counts(dds) + 1), lty = 1, col = colors[colData(dds)$condition],
    lwd = 1, xlab = "log2(Counts + 1)", main = "Raw Counts")
legend("topright", legend = levels(colData(dds)$condition), lwd = 1,
    col = colors)

# plotting an unnormalized box plot of the log transformed
# counts
boxplot(log2(counts(dds) + 1), col = colors[colData(dds)$condition],
    cex.axis = 0.5, las = 1, horizontal = TRUE, xlab = "log2(Counts + 1)",
    ylab = "Samples", main = "Raw Counts")
legend("topright", legend = levels(colData(dds)$condition), lwd = 1,
    col = colors)

Running DESeq

# Run DESeq
dds <- DESeq(dds)

## estimating size factors

## estimating dispersions

## gene-wise dispersion estimates

## mean-dispersion relationship

## final dispersion estimates

## fitting model and testing

# output normalized counts
write.csv(counts(dds, normalize = TRUE), "/Volumes/GoogleDrive/My Drive/Greally_Lab/Toxoplasma/Human/ATAC-Seq/Differential Accessibility/DESeq2_normalized_counts_ATAC.csv",
    row.names = TRUE)

Normalized count distribution

# density plot normalized
plotDensity(log2(counts(dds, normalized = TRUE) + 1), lty = 1,
    col = colors[colData(dds)$condition], lwd = 1, xlab = "log2(Counts + 1)",
    main = "Normalized Counts")
legend("topright", legend = levels(colData(dds)$condition), lwd = 1,
    col = colors)

# box plot normalized
boxplot(log2(counts(dds, normalized = TRUE) + 1), col = colors[colData(dds)$condition],
    cex.axis = 0.5, las = 1, horizontal = TRUE, xlab = "log2(Counts + 1)",
    ylab = "Samples", main = "Normalized Counts")
legend("topright", legend = levels(colData(dds)$condition), lwd = 1,
    col = colors)

Principle Component Analysis

PCA clustering and plotting function

# PCA plot of samples
PCAPlotter <- function(ntop, vsd, shape) {
  # getting most variable genes 
  Pvars <- rowVars(assay(vsd))
  select <- order(Pvars, decreasing = TRUE)[seq_len(min(ntop, 
          length(Pvars)))]
  sampleNO <- rownames(colData(vsd))

  # calculate pca - zero centering variables and scaling where all   variables have unit variance
  PCA <- prcomp(t(assay(vsd)[select, ]), scale = T, center = TRUE)
  percentVar <- round(100*PCA$sdev^2/sum(PCA$sdev^2),1)
  dataGG = data.frame(PC1 = PCA$x[,1], PC2 = PCA$x[,2], 
                      PC3 = PCA$x[,3], PC4 = PCA$x[,4], 
                      condition = colData(vsd)$condition)
  # plotting
  print(ggplot(data = dataGG) +
        geom_point(data = dataGG, mapping = aes(x = PC1, y = PC2, color =  condition, shape = shape), size = 6) +
        scale_shape_identity() +
        labs(title = paste("PC1 vs PC2, Top", toString(ntop), "Variable Peaks"),
        x = paste0("PC1: ", round(percentVar[1],4), "%"),
        y = paste0("PC2: ", round(percentVar[2],4), "%")) +
        #scale_colour_brewer(type="qual", palette=2) +
        scale_colour_viridis(discrete=TRUE) +
        theme_classic() +
        #scale_color_discrete(name = "Condition") +
        theme(axis.text = element_text(size = 15),
        legend.box = "horizontal",
        axis.title.y = element_text(size = 15, face = "bold"),
        axis.title.x = element_text(size = 15, face = "bold"),
        legend.text = element_text(size = 10),
        legend.title = element_text(size = 12, face = "bold"),
        legend.background = element_blank(),
        legend.box.background = element_rect(colour = "black"),
        legend.position = "top") +
        geom_label_repel(aes(label = sampleNO, x = PC1, y = PC2), color = "black") +
        guides(colour = guide_legend(override.aes = list(shape = shape))))
                                     
  PCA$rotation
  PCA$sdev
  return(PCA)
}

Plot PCA

• Using different number of variable genes to see how stable clustering is

dds_vst <- vst(dds)

## -- note: fitType='parametric', but the dispersion trend was not well captured by the
##    function: y = a/x + b, and a local regression fit was automatically substituted.
##    specify fitType='local' or 'mean' to avoid this message next time.

PCA <- PCAPlotter(500, dds_vst, 15)

PCA <- PCAPlotter(1000, dds_vst, 15)

PCA <- PCAPlotter(5000, dds_vst, 15)

PCA <- PCAPlotter(nrow(dds), dds_vst, 15)

PCA <- PCAPlotter(5000, dds_vst, 15)

# get importance of each component
fviz_eig(PCA, addlabels = TRUE)

var <- get_pca_var(PCA)
# contributions of individual genes to each PC
fviz_contrib(PCA, choice = "var", axes = 1, top = 20, rotate = TRUE,
    sort.val = "asc")

fviz_contrib(PCA, choice = "var", axes = 2, top = 20, rotate = TRUE,
    sort.val = "asc")

# contributions of individual samples to each PC
fviz_contrib(PCA, choice = "ind", axes = 1, top = 20, rotate = TRUE,
    sort.val = "asc")

fviz_contrib(PCA, choice = "ind", axes = 2, top = 20, rotate = TRUE,
    sort.val = "asc")

Heatmap of the sample-to-sample distances

sampleDists <- dist(t(assay(dds_vst)))
sampleDistMatrix <- as.matrix(sampleDists)
rownames(sampleDistMatrix) <- paste(colnames(dds_vst))
colnames(sampleDistMatrix) <- paste(colnames(dds_vst))
colors <- magma(255)
pheatmap(sampleDistMatrix, clustering_distance_rows = sampleDists,
    clustering_distance_cols = sampleDists, col = colors)

Removing I1 replicate

• Excluding I1 replicate as this deemed an outlier based on PCA and having low number of toxoplasma reads comapred to other replicates

cnts <- cnts[, -c(1)]

sampleTable <- data.frame(condition = factor(c(rep("Infected",
    2), rep("Uninfected", 3))), row.names = colnames(cnts))

colors <- viridis(6)[c(1, 5)]

dds <- DESeqDataSetFromMatrix(countData = assay(cnts), colData = sampleTable,
    design = ~condition, rowRanges = rowRanges(cnts))
# set control
dds$condition <- relevel(dds$condition, ref = "Uninfected")

dds <- DESeq(dds)

## estimating size factors

## estimating dispersions

## gene-wise dispersion estimates

## mean-dispersion relationship

## final dispersion estimates

## fitting model and testing

Mean Variance Relationship

## Computing mean and variance
norm.counts <- counts(dds, normalized = TRUE)
mean.counts <- rowMeans(norm.counts)
variance.counts <- apply(norm.counts, MARGIN = 1, var)

## Mean and variance relationship
mean.var.col <- densCols(x = log2(mean.counts), y = log2(variance.counts))
plot(x = log2(mean.counts), y = log2(variance.counts), pch = 16,
    cex = 0.5, col = mean.var.col, main = "Mean-variance relationship",
    xlab = "Mean log2(normalized counts) per gene", ylab = "Variance of log2(normalized counts)",
    panel.first = grid())
abline(a = 1, b = 1, col = "red")  # a linear line to compare against

Transform counts to stabilize mean-variance for clustering

Using two transformations in order to stabilize the mean-variance relationship in order to minimize the influence of genes with low read counts when performing unsupervised analysis.

dds_rlog <- rlog(dds)

## -- note: fitType='parametric', but the dispersion trend was not well captured by the
##    function: y = a/x + b, and a local regression fit was automatically substituted.
##    specify fitType='local' or 'mean' to avoid this message next time.

dds_vst <- vst(dds)

## -- note: fitType='parametric', but the dispersion trend was not well captured by the
##    function: y = a/x + b, and a local regression fit was automatically substituted.
##    specify fitType='local' or 'mean' to avoid this message next time.

Log2 transformed counts just for comparison

dds_log2 <- log2(counts(dds) + 1)
meanSdPlot(dds_log2)

## Warning: Computation failed in `stat_binhex()`:

Compare rlog and vst transformations.

meanSdPlot(assay(dds_rlog))

## Warning: Computation failed in `stat_binhex()`:

meanSdPlot(assay(dds_vst))

## Warning: Computation failed in `stat_binhex()`:

## better plot
norm.counts <- assay(dds)
mean.counts <- rowMeans(norm.counts)
variance.counts <- apply(norm.counts, MARGIN = 1, var)
## Mean and variance relationship
mean.var.col <- densCols(x = log2(mean.counts), y = log2(variance.counts))
plot(x = log2(mean.counts), y = log2(variance.counts), pch = 16,
    cex = 0.5, col = mean.var.col, main = "Non-transformed",
    xlab = "Mean log2(normalized counts) per gene", ylab = "Variance of log2(normalized counts)",
    panel.first = grid())

## better plot
norm.counts <- assay(dds_vst)
mean.counts <- rowMeans(norm.counts)
variance.counts <- apply(norm.counts, MARGIN = 1, var)
## Mean and variance relationship
mean.var.col <- densCols(x = log2(mean.counts), y = log2(variance.counts))
plot(x = log2(mean.counts), y = log2(variance.counts), pch = 16,
    cex = 0.5, col = mean.var.col, main = "VST transformed",
    xlab = "Mean log2(normalized counts) per gene", ylab = "Variance of log2(normalized counts)",
    panel.first = grid())

write.csv(assay(dds_vst), "/Volumes/GoogleDrive/My Drive/Greally_Lab/Toxoplasma/Human/ATAC-Seq/Differential Accessibility//DESeq2_vst_counts_ATAC.csv",
    row.names = TRUE)

Plot PCA

• Using different number of variable genes to see how stable clustering is

PCA <- PCAPlotter(500, dds_vst, 15)

PCA <- PCAPlotter(1000, dds_vst, 15)

PCA <- PCAPlotter(5000, dds_vst, 15)

PCA <- PCAPlotter(nrow(dds), dds_vst, 15)

PCA <- PCAPlotter(5000, dds_vst, 15)

# get importance of each component
fviz_eig(PCA, addlabels = TRUE)

var <- get_pca_var(PCA)
# contributions of individual genes to each PC
fviz_contrib(PCA, choice = "var", axes = 1, top = 20, rotate = TRUE,
    sort.val = "asc")

fviz_contrib(PCA, choice = "var", axes = 2, top = 20, rotate = TRUE,
    sort.val = "asc")

# contributions of individual samples to each PC
fviz_contrib(PCA, choice = "ind", axes = 1, top = 20, rotate = TRUE,
    sort.val = "asc")

fviz_contrib(PCA, choice = "ind", axes = 2, top = 20, rotate = TRUE,
    sort.val = "asc")

Heatmap of the sample-to-sample distances

sampleDists <- dist(t(assay(dds_vst)))
sampleDistMatrix <- as.matrix(sampleDists)
rownames(sampleDistMatrix) <- paste(colnames(dds_vst))
colnames(sampleDistMatrix) <- paste(colnames(dds_vst))
colors <- magma(255)
pheatmap(sampleDistMatrix, clustering_distance_rows = sampleDists,
    clustering_distance_cols = sampleDists, col = colors)

Differential Accessibility Results

Output function

writeOutput <- function(res, cond, dir) {
    resOrdered <- res[order(res$padj), ]
    outfile <- paste(cond[1], cond[length(cond)], "DESeq2.csv",
        sep = "_")
    outfile <- paste(dir, outfile, sep = "")
    write.csv(as.data.frame(resOrdered), file = outfile, row.names = TRUE)
}

# setting output dir
dir <- "/Volumes/GoogleDrive/My Drive/Greally_Lab/Toxoplasma/Human/ATAC-Seq/Differential Accessibility/"

Infected vs Uninfected

res <- results(dds, alpha = 0.05, name = "condition_Infected_vs_Uninfected")
res.granges <- results(dds, alpha = 0.05, name = "condition_Infected_vs_Uninfected",
    format = "GRanges")

# p-value distribution histogram
hist(res.granges$pvalue, main = "P-value distribution", xlab = "P-value",
    ylab = "Frequency", col = "lavender")

summary(res, alpha = 0.05)

## 
## out of 26706 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0 (up)       : 503, 1.9%
## LFC < 0 (down)     : 27, 0.1%
## outliers [1]       : 0, 0%
## low counts [2]     : 0, 0%
## (mean count < 1)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results

# ma plot
plotMA(res)

# get shrunken fold change
res.lfcShrink <- lfcShrink(dds = dds, res = res, contrast = c("condition",
    "Infected", "Uninfected"), type = "ashr")

## using 'ashr' for LFC shrinkage. If used in published research, please cite:
##     Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
##     https://doi.org/10.1093/biostatistics/kxw041

res.lfcShrink.granges <- lfcShrink(dds = dds, res = res, contrast = c("condition",
    "Infected", "Uninfected"), type = "ashr", format = "GRanges")

## using 'ashr' for LFC shrinkage. If used in published research, please cite:
##     Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
##     https://doi.org/10.1093/biostatistics/kxw041

summary(res.lfcShrink, alpha = 0.05)

## 
## out of 26706 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0 (up)       : 503, 1.9%
## LFC < 0 (down)     : 27, 0.1%
## outliers [1]       : 0, 0%
## low counts [2]     : 0, 0%
## (mean count < 1)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results

# ma plot
plotMA(res.lfcShrink)

# look at most differentially accessible
plotCounts(dds, gene = which.min(res$padj), intgroup = "condition")

# add counts
res.lfcShrink.granges@elementMetadata <- cbind(res.lfcShrink.granges@elementMetadata,
    counts(dds, normalized = TRUE))

writeOutput(res.lfcShrink.granges, c("Uninfected", "Infected_ALL"),
    dir)

Unannotated results

MA plot

cutoff <- sort(res.lfcShrink.granges$padj)[20]
df <- as.data.frame(res.lfcShrink.granges)

ggplot(df, aes(x = log2(baseMean), y = log2FoldChange)) + geom_point(aes(colour = padj <
    0.05), shape = 20, size = 0.5) + labs(x = "mean of normalised counts",
    y = "log fold change") + ylim(-2, 6) + theme_classic()

Volcano plot

EnhancedVolcano(res, lab = "", x = "log2FoldChange", y = "pvalue",
    xlim = c(-2.5, 6), pCutoff = 0.05, pCutoffCol = "padj", FCcutoff = 2,
    drawConnectors = TRUE, maxoverlapsConnectors = Inf, title = "",
    subtitle = "", gridlines.minor = FALSE, gridlines.major = FALSE,
    col = c("black", "black", "black", "red3"), raster = TRUE)

Heatmap

# omit NAs 
res <- na.omit(res)
# set up matrix
dds_vst.mat <- as.matrix(assay(dds_vst))
dds_vst.mat <- dds_vst.mat[,c(3,4,5,1,2)]
# getting differentially expressed genes 
dds_vst.mat.DE <- dds_vst.mat[which(res$padj < 0.05),]

colors <- viridis(5)[c(1,5)]
col <- list(Condition = c(
            "Uninfected" = colors[1],
            "Infected" = colors[2]))

condition <- factor(c(rep("Uninfected", 3), rep("Infected", 2)), levels = c("Uninfected", "Infected"))
ha <- HeatmapAnnotation(Condition = condition, col = col)

scaled.mat <- t(scale(t(dds_vst.mat.DE),center=TRUE,scale=TRUE))

Heatmap(scaled.mat,
        name = "Z-score", #title of legend
        #col=magma(100),
        row_names_gp = gpar(fontsize = 7), # Text size for row names
        top_annotation = ha,
        border = TRUE,
        cluster_rows = TRUE,
        cluster_columns = FALSE,
        show_row_names = FALSE,
        column_names_rot = 0,
        show_parent_dend_line = FALSE,
        row_dend_width = unit(20, "mm"))

Plot accessibility changes over chromosomes

res.lfcShrink.granges.plot <- res.lfcShrink.granges
mcols(res.lfcShrink.granges.plot)$score <- -log10(res.lfcShrink.granges.plot$padj)
res.lfcShrink.granges.plot <- keepSeqlevels(res.lfcShrink.granges.plot,
    pruning.mode = "tidy", c(paste0("chr", 1:21), "chrX", "chrY"))

plotGrandLinear(res.lfcShrink.granges.plot, aes(y = score), color = turbo(2),
    cutoff = -log10(0.05), cutoff.color = "black", cutoff.size = 1,
    ylab = "-log10(padj)", spaceline = TRUE, highlight.label.size = 3,
    highlight.label.offset = 0.01) + theme(axis.text.x = element_text(angle = 45,
    hjust = 1))

## using coord:genome to parse x scale

autoplot(res.lfcShrink.granges.plot[res.lfcShrink.granges.plot$padj <
    0.05, ], layout = "karyogram", aes(color = log2FoldChange,
    fill = log2FoldChange)) + scale_color_gradient(low = "blue",
    high = "red") + scale_fill_gradient(low = "blue", high = "red")

## Warning in getIdeoGR(data): geom(ideogram) need valid seqlengths information for accurate mapping,
##                  now use reduced information as ideogram...

## Warning in getIdeoGR(data): geom(ideogram) need valid seqlengths information for accurate mapping,
##                  now use reduced information as ideogram...

## Scale for 'x' is already present. Adding another scale for 'x', which will
## replace the existing scale.

## Scale for 'x' is already present. Adding another scale for 'x', which will
## replace the existing scale.

Review peak results in IGV

res.lfcShrink.granges <- res.lfcShrink.granges[order(res.lfcShrink.granges$padj),
    ]
makebedtable(res.lfcShrink.granges, "res.lfcShrink.granges.html",
    dir)

## [1] "/Volumes/GoogleDrive/My Drive/Greally_Lab/Toxoplasma/Human/ATAC-Seq/Differential Accessibility//res.lfcShrink.granges.html"

Plot distribution over features

if (require(TxDb.Hsapiens.UCSC.hg38.knownGene)) {
    aCR <- assignChromosomeRegion(res.lfcShrink.granges[res.lfcShrink.granges$padj <
        0.05, ], nucleotideLevel = FALSE, precedence = c("Promoters",
        "immediateDownstream", "fiveUTRs", "threeUTRs", "Exons",
        "Introns"), TxDb = TxDb.Hsapiens.UCSC.hg38.knownGene)
    barplot(aCR$percentage)
    pie1(aCR$percentage)
}

## Warning in
## assignChromosomeRegion(res.lfcShrink.granges[res.lfcShrink.granges$padj < :
## peaks.RD has sequence levels not in TxDb.

Plot distance of DAR to TSS

res.lfcShrink.granges.ChIPseeker <- annotatePeak(res.lfcShrink.granges[res.lfcShrink.granges$padj <
    0.05], tssRegion = c(-5000, 5000), flankDistance = 5000,
    TxDb = TxDb.Hsapiens.UCSC.hg38.knownGene, annoDb = "org.Hs.eg.db",
    overlap = "TSS", level = "gene")

## >> preparing features information...      2022-04-20 11:22:33 
## >> identifying nearest features...        2022-04-20 11:22:34

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': JTFH01000247.1, JTFH01000515.1, JTFH01000804.1, JTFH01000876.1, JTFH01001024.1, JTFH01001390.1, JTFH01001405.1, JTFH01001430.1, JTFH01001465.1, JTFH01001478.1, JTFH01001512.1, JTFH01001549.1, JTFH01001680.1, JTFH01001724.1, JTFH01001862.1, JTFH01001929.1, JTFH01001959.1, JTFH01001981.1, JTFH01001998.1, KN707720.1, KN707809.1, KN707828.1, KN707893.1, KN707896.1, JTFH01000028.1, JTFH01000280.1, JTFH01000942.1, JTFH01001023.1, JTFH01001317.1, JTFH01001613.1, JTFH01001899.1, KN707626.1
##   - in 'y': chrM, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270706v1_random, chr1_KI270707v1_random, chr1_KI270708v1_random, chr1_KI270709v1_random, chr1_KI270710v1_random, chr1_KI270711v1_random, chr1_KI270712v1_random, chr1_KI270714v1_random, chr1_KI270759v1_alt, chr1_KI270760v1_alt, chr1_KI270761v1_alt, chr1_KI270762v1_alt, chr1_KI270763v1_alt, chr1_KI270764v1_alt, chr1_KI270765v1_alt, chr1_KI270766v1_alt, chr1_KI270892v1_alt, chr1_KN196472v1_fix, chr1_KN196473v1_fix, chr1_KN196474v1_fix, chr1_KN538360v1_fix, chr1_KN538361v1_fix, chr1_KQ031383v1_fix, chr1_KQ458382v1_alt, chr1_KQ458383v1_alt, chr1_KQ458384v1_alt, chr1_KQ983255v1_alt, chr1_KV880763v1_alt, chr1_KZ208904v1_alt, chr1_KZ208905v1_alt, chr1_KZ208906v1_fix, chr1_KZ559100v1_fix, chr2_GL383521v1_alt, chr2_GL383522v1_alt, chr2_GL582966v2_alt, chr2_KI270715v1_random, chr2_KI270716v1_random, chr2_KI270767v1_alt, chr2_KI270768v1_alt, chr2_KI270769v1_alt, chr2_KI270770v1_alt, chr2_KI270771v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270775v1_alt, chr2_KI270776v1_alt, chr2_KI270893v1_alt, chr2_KI270894v1_alt, chr2_KN538362v1_fix, chr2_KN538363v1_fix, chr2_KQ031384v1_fix, chr2_KQ983256v1_alt, chr2_KZ208907v1_alt, chr2_KZ208908v1_alt, chr2_ML143341v1_fix, chr2_ML143342v1_fix, chr3_GL000221v1_random, chr3_GL383526v1_alt, chr3_JH636055v2_alt, chr3_KI270777v1_alt, chr3_KI270778v1_alt, chr3_KI270779v1_alt, chr3_KI270780v1_alt, chr3_KI270781v1_alt, chr3_KI270782v1_alt, chr3_KI270783v1_alt, chr3_KI270784v1_alt, chr3_KI270895v1_alt, chr3_KI270924v1_alt, chr3_KI270934v1_alt, chr3_KI270935v1_alt, chr3_KI270936v1_alt, chr3_KI270937v1_alt, chr3_KN196475v1_fix, chr3_KN196476v1_fix, chr3_KN538364v1_fix, chr3_KQ031385v1_fix, chr3_KQ031386v1_fix, chr3_KV766192v1_fix, chr3_KZ208909v1_alt, chr3_KZ559101v1_alt, chr3_KZ559102v1_alt, chr3_KZ559103v1_alt, chr3_KZ559104v1_fix, chr3_KZ559105v1_alt, chr3_ML143343v1_alt, chr4_GL000008v2_random, chr4_GL000257v2_alt, chr4_GL383528v1_alt, chr4_KI270785v1_alt, chr4_KI270786v1_alt, chr4_KI270787v1_alt, chr4_KI270788v1_alt, chr4_KI270789v1_alt, chr4_KI270790v1_alt, chr4_KI270896v1_alt, chr4_KI270925v1_alt, chr4_KQ090013v1_alt, chr4_KQ090014v1_alt, chr4_KQ090015v1_alt, chr4_KQ983257v1_fix, chr4_KQ983258v1_alt, chr4_KV766193v1_alt, chr4_ML143344v1_fix, chr4_ML143345v1_fix, chr4_ML143346v1_fix, chr4_ML143347v1_fix, chr4_ML143348v1_fix, chr4_ML143349v1_fix, chr5_GL000208v1_random, chr5_GL383530v1_alt, chr5_GL383531v1_alt, chr5_GL383532v1_alt, chr5_GL949742v1_alt, chr5_KI270791v1_alt, chr5_KI270792v1_alt, chr5_KI270793v1_alt, chr5_KI270794v1_alt, chr5_KI270795v1_alt, chr5_KI270796v1_alt, chr5_KI270897v1_alt, chr5_KI270898v1_alt, chr5_KN196477v1_alt, chr5_KV575243v1_alt, chr5_KV575244v1_fix, chr5_KZ208910v1_alt, chr5_ML143350v1_fix, chr6_GL000250v2_alt, chr6_GL000252v2_alt, chr6_GL000253v2_alt, chr6_GL000254v2_alt, chr6_GL000255v2_alt, chr6_GL000256v2_alt, chr6_GL383533v1_alt, chr6_KB021644v2_alt, chr6_KI270758v1_alt, chr6_KI270797v1_alt, chr6_KI270799v1_alt, chr6_KI270800v1_alt, chr6_KI270801v1_alt, chr6_KI270802v1_alt, chr6_KN196478v1_fix, chr6_KQ031387v1_fix, chr6_KQ090016v1_fix, chr6_KQ090017v1_alt, chr6_KV766194v1_fix, chr6_KZ208911v1_fix, chr6_ML143351v1_fix, chr7_GL383534v2_alt, chr7_KI270805v1_alt, chr7_KI270806v1_alt, chr7_KI270807v1_alt, chr7_KI270808v1_alt, chr7_KI270809v1_alt, chr7_KI270899v1_alt, chr7_KQ031388v1_fix, chr7_KV880764v1_fix, chr7_KV880765v1_fix, chr7_KZ208912v1_fix, chr7_KZ208913v1_alt, chr7_KZ559106v1_alt, chr7_ML143352v1_fix, chr8_KI270810v1_alt, chr8_KI270811v1_alt, chr8_KI270812v1_alt, chr8_KI270814v1_alt, chr8_KI270815v1_alt, chr8_KI270816v1_alt, chr8_KI270817v1_alt, chr8_KI270818v1_alt, chr8_KI270819v1_alt, chr8_KI270820v1_alt, chr8_KI270822v1_alt, chr8_KI270900v1_alt, chr8_KI270901v1_alt, chr8_KI270926v1_alt, chr8_KV880766v1_fix, chr8_KV880767v1_fix, chr8_KZ208914v1_fix, chr8_KZ208915v1_fix, chr8_KZ559107v1_alt, chr9_GL383540v1_alt, chr9_GL383541v1_alt, chr9_GL383542v1_alt, chr9_KI270717v1_random, chr9_KI270718v1_random, chr9_KI270719v1_random, chr9_KI270720v1_random, chr9_KI270823v1_alt, chr9_KN196479v1_fix, chr9_KQ090018v1_alt, chr9_KQ090019v1_alt, chr9_ML143353v1_fix, chr10_GL383545v1_alt, chr10_GL383546v1_alt, chr10_KI270824v1_alt, chr10_KI270825v1_alt, chr10_KN196480v1_fix, chr10_KN538365v1_fix, chr10_KN538366v1_fix, chr10_KN538367v1_fix, chr10_KQ090020v1_alt, chr10_KQ090021v1_fix, chr10_ML143354v1_fix, chr10_ML143355v1_fix, chr11_GL383547v1_alt, chr11_JH159136v1_alt, chr11_JH159137v1_alt, chr11_KI270721v1_random, chr11_KI270826v1_alt, chr11_KI270827v1_alt, chr11_KI270829v1_alt, chr11_KI270831v1_alt, chr11_KI270832v1_alt, chr11_KI270902v1_alt, chr11_KI270903v1_alt, chr11_KI270927v1_alt, chr11_KN196481v1_fix, chr11_KN538368v1_alt, chr11_KQ090022v1_fix, chr11_KQ759759v1_fix, chr11_KV766195v1_fix, chr11_KZ559108v1_fix, chr11_KZ559109v1_fix, chr11_KZ559110v1_alt, chr11_KZ559111v1_alt, chr11_ML143356v1_fix, chr11_ML143357v1_fix, chr11_ML143358v1_fix, chr11_ML143359v1_fix, chr11_ML143360v1_fix, chr12_GL383549v1_alt, chr12_GL383550v2_alt, chr12_GL383551v1_alt, chr12_GL383552v1_alt, chr12_GL877875v1_alt, chr12_GL877876v1_alt, chr12_KI270833v1_alt, chr12_KI270834v1_alt, chr12_KI270835v1_alt, chr12_KI270836v1_alt, chr12_KI270837v1_alt, chr12_KI270904v1_alt, chr12_KN196482v1_fix, chr12_KN538369v1_fix, chr12_KN538370v1_fix, chr12_KQ090023v1_alt, chr12_KQ759760v1_fix, chr12_KZ208916v1_fix, chr12_KZ208917v1_fix, chr12_KZ208918v1_alt, chr12_KZ559112v1_alt, chr12_ML143361v1_fix, chr12_ML143362v1_fix, chr13_KI270838v1_alt, chr13_KI270839v1_alt, chr13_KI270840v1_alt, chr13_KI270841v1_alt, chr13_KI270842v1_alt, chr13_KI270843v1_alt, chr13_KN196483v1_fix, chr13_KN538371v1_fix, chr13_KN538372v1_fix, chr13_KN538373v1_fix, chr13_KQ090024v1_alt, chr13_KQ090025v1_alt, chr13_ML143363v1_fix, chr13_ML143364v1_fix, chr13_ML143365v1_fix, chr13_ML143366v1_fix, chr14_GL000009v2_random, chr14_GL000194v1_random, chr14_KI270722v1_random, chr14_KI270723v1_random, chr14_KI270724v1_random, chr14_KI270725v1_random, chr14_KI270726v1_random, chr14_KI270844v1_alt, chr14_KI270845v1_alt, chr14_KI270846v1_alt, chr14_KI270847v1_alt, chr14_KZ208919v1_alt, chr14_KZ208920v1_fix, chr14_ML143367v1_fix, chr14_ML143368v1_alt, chr15_GL383554v1_alt, chr15_GL383555v2_alt, chr15_KI270727v1_random, chr15_KI270848v1_alt, chr15_KI270849v1_alt, chr15_KI270851v1_alt, chr15_KI270852v1_alt, chr15_KI270906v1_alt, chr15_KN538374v1_fix, chr15_KQ031389v1_alt, chr15_ML143369v1_fix, chr15_ML143370v1_fix, chr15_ML143371v1_fix, chr15_ML143372v1_fix, chr16_GL383556v1_alt, chr16_GL383557v1_alt, chr16_KI270728v1_random, chr16_KI270854v1_alt, chr16_KI270855v1_alt, chr16_KI270856v1_alt, chr16_KQ031390v1_alt, chr16_KQ090026v1_alt, chr16_KQ090027v1_alt, chr16_KV880768v1_fix, chr16_KZ208921v1_alt, chr16_KZ559113v1_fix, chr16_ML143373v1_fix, chr17_GL000258v2_alt, chr17_GL383563v3_alt, chr17_GL383564v2_alt, chr17_GL383565v1_alt, chr17_GL383566v1_alt, chr17_JH159146v1_alt, chr17_JH159147v1_alt, chr17_JH159148v1_alt, chr17_KI270730v1_random, chr17_KI270857v1_alt, chr17_KI270858v1_alt, chr17_KI270859v1_alt, chr17_KI270860v1_alt, chr17_KI270861v1_alt, chr17_KI270862v1_alt, chr17_KI270907v1_alt, chr17_KI270908v1_alt, chr17_KI270909v1_alt, chr17_KI270910v1_alt, chr17_KV575245v1_fix, chr17_KV766196v1_fix, chr17_KV766197v1_alt, chr17_KV766198v1_alt, chr17_KZ559114v1_alt, chr17_ML143374v1_fix, chr17_ML143375v1_fix, chr18_GL383567v1_alt, chr18_GL383568v1_alt, chr18_GL383569v1_alt, chr18_GL383570v1_alt, chr18_GL383571v1_alt, chr18_GL383572v1_alt, chr18_KI270863v1_alt, chr18_KI270864v1_alt, chr18_KI270911v1_alt, chr18_KI270912v1

## >> calculating distance from peak to TSS...   2022-04-20 11:22:34 
## >> assigning genomic annotation...        2022-04-20 11:22:34

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': JTFH01000247.1, JTFH01000515.1, JTFH01000804.1, JTFH01000876.1, JTFH01001024.1, JTFH01001390.1, JTFH01001405.1, JTFH01001430.1, JTFH01001465.1, JTFH01001478.1, JTFH01001512.1, JTFH01001549.1, JTFH01001680.1, JTFH01001724.1, JTFH01001862.1, JTFH01001929.1, JTFH01001959.1, JTFH01001981.1, JTFH01001998.1, KN707720.1, KN707809.1, KN707828.1, KN707893.1, KN707896.1, JTFH01000028.1, JTFH01000280.1, JTFH01000942.1, JTFH01001023.1, JTFH01001317.1, JTFH01001613.1, JTFH01001899.1, KN707626.1
##   - in 'y': chrM, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270706v1_random, chr1_KI270707v1_random, chr1_KI270708v1_random, chr1_KI270709v1_random, chr1_KI270710v1_random, chr1_KI270711v1_random, chr1_KI270712v1_random, chr1_KI270714v1_random, chr1_KI270759v1_alt, chr1_KI270760v1_alt, chr1_KI270761v1_alt, chr1_KI270762v1_alt, chr1_KI270763v1_alt, chr1_KI270764v1_alt, chr1_KI270765v1_alt, chr1_KI270766v1_alt, chr1_KI270892v1_alt, chr1_KN196472v1_fix, chr1_KN196473v1_fix, chr1_KN196474v1_fix, chr1_KN538360v1_fix, chr1_KN538361v1_fix, chr1_KQ031383v1_fix, chr1_KQ458382v1_alt, chr1_KQ458383v1_alt, chr1_KQ458384v1_alt, chr1_KQ983255v1_alt, chr1_KV880763v1_alt, chr1_KZ208904v1_alt, chr1_KZ208905v1_alt, chr1_KZ208906v1_fix, chr1_KZ559100v1_fix, chr2_GL383521v1_alt, chr2_GL383522v1_alt, chr2_GL582966v2_alt, chr2_KI270715v1_random, chr2_KI270716v1_random, chr2_KI270767v1_alt, chr2_KI270768v1_alt, chr2_KI270769v1_alt, chr2_KI270770v1_alt, chr2_KI270771v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270775v1_alt, chr2_KI270776v1_alt, chr2_KI270893v1_alt, chr2_KI270894v1_alt, chr2_KN538362v1_fix, chr2_KN538363v1_fix, chr2_KQ031384v1_fix, chr2_KQ983256v1_alt, chr2_KZ208907v1_alt, chr2_KZ208908v1_alt, chr2_ML143341v1_fix, chr2_ML143342v1_fix, chr3_GL000221v1_random, chr3_GL383526v1_alt, chr3_JH636055v2_alt, chr3_KI270777v1_alt, chr3_KI270778v1_alt, chr3_KI270779v1_alt, chr3_KI270780v1_alt, chr3_KI270781v1_alt, chr3_KI270782v1_alt, chr3_KI270783v1_alt, chr3_KI270784v1_alt, chr3_KI270895v1_alt, chr3_KI270924v1_alt, chr3_KI270934v1_alt, chr3_KI270935v1_alt, chr3_KI270936v1_alt, chr3_KI270937v1_alt, chr3_KN196475v1_fix, chr3_KN196476v1_fix, chr3_KN538364v1_fix, chr3_KQ031385v1_fix, chr3_KQ031386v1_fix, chr3_KV766192v1_fix, chr3_KZ208909v1_alt, chr3_KZ559101v1_alt, chr3_KZ559102v1_alt, chr3_KZ559103v1_alt, chr3_KZ559104v1_fix, chr3_KZ559105v1_alt, chr3_ML143343v1_alt, chr4_GL000008v2_random, chr4_GL000257v2_alt, chr4_GL383528v1_alt, chr4_KI270785v1_alt, chr4_KI270786v1_alt, chr4_KI270787v1_alt, chr4_KI270788v1_alt, chr4_KI270789v1_alt, chr4_KI270790v1_alt, chr4_KI270896v1_alt, chr4_KI270925v1_alt, chr4_KQ090013v1_alt, chr4_KQ090014v1_alt, chr4_KQ090015v1_alt, chr4_KQ983257v1_fix, chr4_KQ983258v1_alt, chr4_KV766193v1_alt, chr4_ML143344v1_fix, chr4_ML143345v1_fix, chr4_ML143346v1_fix, chr4_ML143347v1_fix, chr4_ML143348v1_fix, chr4_ML143349v1_fix, chr5_GL000208v1_random, chr5_GL383530v1_alt, chr5_GL383531v1_alt, chr5_GL383532v1_alt, chr5_GL949742v1_alt, chr5_KI270791v1_alt, chr5_KI270792v1_alt, chr5_KI270793v1_alt, chr5_KI270794v1_alt, chr5_KI270795v1_alt, chr5_KI270796v1_alt, chr5_KI270897v1_alt, chr5_KI270898v1_alt, chr5_KN196477v1_alt, chr5_KV575243v1_alt, chr5_KV575244v1_fix, chr5_KZ208910v1_alt, chr5_ML143350v1_fix, chr6_GL000250v2_alt, chr6_GL000252v2_alt, chr6_GL000253v2_alt, chr6_GL000254v2_alt, chr6_GL000255v2_alt, chr6_GL000256v2_alt, chr6_GL383533v1_alt, chr6_KB021644v2_alt, chr6_KI270758v1_alt, chr6_KI270797v1_alt, chr6_KI270799v1_alt, chr6_KI270800v1_alt, chr6_KI270801v1_alt, chr6_KI270802v1_alt, chr6_KN196478v1_fix, chr6_KQ031387v1_fix, chr6_KQ090016v1_fix, chr6_KQ090017v1_alt, chr6_KV766194v1_fix, chr6_KZ208911v1_fix, chr6_ML143351v1_fix, chr7_GL383534v2_alt, chr7_KI270805v1_alt, chr7_KI270806v1_alt, chr7_KI270807v1_alt, chr7_KI270808v1_alt, chr7_KI270809v1_alt, chr7_KI270899v1_alt, chr7_KQ031388v1_fix, chr7_KV880764v1_fix, chr7_KV880765v1_fix, chr7_KZ208912v1_fix, chr7_KZ208913v1_alt, chr7_KZ559106v1_alt, chr7_ML143352v1_fix, chr8_KI270810v1_alt, chr8_KI270811v1_alt, chr8_KI270812v1_alt, chr8_KI270814v1_alt, chr8_KI270815v1_alt, chr8_KI270816v1_alt, chr8_KI270817v1_alt, chr8_KI270818v1_alt, chr8_KI270819v1_alt, chr8_KI270820v1_alt, chr8_KI270822v1_alt, chr8_KI270900v1_alt, chr8_KI270901v1_alt, chr8_KI270926v1_alt, chr8_KV880766v1_fix, chr8_KV880767v1_fix, chr8_KZ208914v1_fix, chr8_KZ208915v1_fix, chr8_KZ559107v1_alt, chr9_GL383540v1_alt, chr9_GL383541v1_alt, chr9_GL383542v1_alt, chr9_KI270717v1_random, chr9_KI270718v1_random, chr9_KI270719v1_random, chr9_KI270720v1_random, chr9_KI270823v1_alt, chr9_KN196479v1_fix, chr9_KQ090018v1_alt, chr9_KQ090019v1_alt, chr9_ML143353v1_fix, chr10_GL383545v1_alt, chr10_GL383546v1_alt, chr10_KI270824v1_alt, chr10_KI270825v1_alt, chr10_KN196480v1_fix, chr10_KN538365v1_fix, chr10_KN538366v1_fix, chr10_KN538367v1_fix, chr10_KQ090020v1_alt, chr10_KQ090021v1_fix, chr10_ML143354v1_fix, chr10_ML143355v1_fix, chr11_GL383547v1_alt, chr11_JH159136v1_alt, chr11_JH159137v1_alt, chr11_KI270721v1_random, chr11_KI270826v1_alt, chr11_KI270827v1_alt, chr11_KI270829v1_alt, chr11_KI270831v1_alt, chr11_KI270832v1_alt, chr11_KI270902v1_alt, chr11_KI270903v1_alt, chr11_KI270927v1_alt, chr11_KN196481v1_fix, chr11_KN538368v1_alt, chr11_KQ090022v1_fix, chr11_KQ759759v1_fix, chr11_KV766195v1_fix, chr11_KZ559108v1_fix, chr11_KZ559109v1_fix, chr11_KZ559110v1_alt, chr11_KZ559111v1_alt, chr11_ML143356v1_fix, chr11_ML143357v1_fix, chr11_ML143358v1_fix, chr11_ML143359v1_fix, chr11_ML143360v1_fix, chr12_GL383549v1_alt, chr12_GL383550v2_alt, chr12_GL383551v1_alt, chr12_GL383552v1_alt, chr12_GL877875v1_alt, chr12_GL877876v1_alt, chr12_KI270833v1_alt, chr12_KI270834v1_alt, chr12_KI270835v1_alt, chr12_KI270836v1_alt, chr12_KI270837v1_alt, chr12_KI270904v1_alt, chr12_KN196482v1_fix, chr12_KN538369v1_fix, chr12_KN538370v1_fix, chr12_KQ090023v1_alt, chr12_KQ759760v1_fix, chr12_KZ208916v1_fix, chr12_KZ208917v1_fix, chr12_KZ208918v1_alt, chr12_KZ559112v1_alt, chr12_ML143361v1_fix, chr12_ML143362v1_fix, chr13_KI270838v1_alt, chr13_KI270839v1_alt, chr13_KI270840v1_alt, chr13_KI270841v1_alt, chr13_KI270842v1_alt, chr13_KI270843v1_alt, chr13_KN196483v1_fix, chr13_KN538371v1_fix, chr13_KN538372v1_fix, chr13_KN538373v1_fix, chr13_KQ090024v1_alt, chr13_KQ090025v1_alt, chr13_ML143363v1_fix, chr13_ML143364v1_fix, chr13_ML143365v1_fix, chr13_ML143366v1_fix, chr14_GL000009v2_random, chr14_GL000194v1_random, chr14_KI270722v1_random, chr14_KI270723v1_random, chr14_KI270724v1_random, chr14_KI270725v1_random, chr14_KI270726v1_random, chr14_KI270844v1_alt, chr14_KI270845v1_alt, chr14_KI270846v1_alt, chr14_KI270847v1_alt, chr14_KZ208919v1_alt, chr14_KZ208920v1_fix, chr14_ML143367v1_fix, chr14_ML143368v1_alt, chr15_GL383554v1_alt, chr15_GL383555v2_alt, chr15_KI270727v1_random, chr15_KI270848v1_alt, chr15_KI270849v1_alt, chr15_KI270851v1_alt, chr15_KI270852v1_alt, chr15_KI270906v1_alt, chr15_KN538374v1_fix, chr15_KQ031389v1_alt, chr15_ML143369v1_fix, chr15_ML143370v1_fix, chr15_ML143371v1_fix, chr15_ML143372v1_fix, chr16_GL383556v1_alt, chr16_GL383557v1_alt, chr16_KI270728v1_random, chr16_KI270854v1_alt, chr16_KI270855v1_alt, chr16_KI270856v1_alt, chr16_KQ031390v1_alt, chr16_KQ090026v1_alt, chr16_KQ090027v1_alt, chr16_KV880768v1_fix, chr16_KZ208921v1_alt, chr16_KZ559113v1_fix, chr16_ML143373v1_fix, chr17_GL000258v2_alt, chr17_GL383563v3_alt, chr17_GL383564v2_alt, chr17_GL383565v1_alt, chr17_GL383566v1_alt, chr17_JH159146v1_alt, chr17_JH159147v1_alt, chr17_JH159148v1_alt, chr17_KI270730v1_random, chr17_KI270857v1_alt, chr17_KI270858v1_alt, chr17_KI270859v1_alt, chr17_KI270860v1_alt, chr17_KI270861v1_alt, chr17_KI270862v1_alt, chr17_KI270907v1_alt, chr17_KI270908v1_alt, chr17_KI270909v1_alt, chr17_KI270910v1_alt, chr17_KV575245v1_fix, chr17_KV766196v1_fix, chr17_KV766197v1_alt, chr17_KV766198v1_alt, chr17_KZ559114v1_alt, chr17_ML143374v1_fix, chr17_ML143375v1_fix, chr18_GL383567v1_alt, chr18_GL383568v1_alt, chr18_GL383569v1_alt, chr18_GL383570v1_alt, chr18_GL383571v1_alt, chr18_GL383572v1_alt, chr18_KI270863v1_alt, chr18_KI270864v1_alt, chr18_KI270911v1_alt, chr18_KI270912v1

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': JTFH01000247.1, JTFH01000515.1, JTFH01000804.1, JTFH01000876.1, JTFH01001024.1, JTFH01001390.1, JTFH01001405.1, JTFH01001430.1, JTFH01001465.1, JTFH01001478.1, JTFH01001512.1, JTFH01001549.1, JTFH01001680.1, JTFH01001724.1, JTFH01001862.1, JTFH01001929.1, JTFH01001959.1, JTFH01001981.1, JTFH01001998.1, KN707720.1, KN707809.1, KN707828.1, KN707893.1, KN707896.1, JTFH01000028.1, JTFH01000280.1, JTFH01000942.1, JTFH01001023.1, JTFH01001317.1, JTFH01001613.1, JTFH01001899.1, KN707626.1
##   - in 'y': chrM, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270706v1_random, chr1_KI270707v1_random, chr1_KI270708v1_random, chr1_KI270709v1_random, chr1_KI270710v1_random, chr1_KI270711v1_random, chr1_KI270712v1_random, chr1_KI270714v1_random, chr1_KI270759v1_alt, chr1_KI270760v1_alt, chr1_KI270761v1_alt, chr1_KI270762v1_alt, chr1_KI270763v1_alt, chr1_KI270764v1_alt, chr1_KI270765v1_alt, chr1_KI270766v1_alt, chr1_KI270892v1_alt, chr1_KN196472v1_fix, chr1_KN196473v1_fix, chr1_KN196474v1_fix, chr1_KN538360v1_fix, chr1_KN538361v1_fix, chr1_KQ031383v1_fix, chr1_KQ458382v1_alt, chr1_KQ458383v1_alt, chr1_KQ458384v1_alt, chr1_KQ983255v1_alt, chr1_KV880763v1_alt, chr1_KZ208904v1_alt, chr1_KZ208905v1_alt, chr1_KZ208906v1_fix, chr1_KZ559100v1_fix, chr2_GL383521v1_alt, chr2_GL383522v1_alt, chr2_GL582966v2_alt, chr2_KI270715v1_random, chr2_KI270716v1_random, chr2_KI270767v1_alt, chr2_KI270768v1_alt, chr2_KI270769v1_alt, chr2_KI270770v1_alt, chr2_KI270771v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270775v1_alt, chr2_KI270776v1_alt, chr2_KI270893v1_alt, chr2_KI270894v1_alt, chr2_KN538362v1_fix, chr2_KN538363v1_fix, chr2_KQ031384v1_fix, chr2_KQ983256v1_alt, chr2_KZ208907v1_alt, chr2_KZ208908v1_alt, chr2_ML143341v1_fix, chr2_ML143342v1_fix, chr3_GL000221v1_random, chr3_GL383526v1_alt, chr3_JH636055v2_alt, chr3_KI270777v1_alt, chr3_KI270778v1_alt, chr3_KI270779v1_alt, chr3_KI270780v1_alt, chr3_KI270781v1_alt, chr3_KI270782v1_alt, chr3_KI270783v1_alt, chr3_KI270784v1_alt, chr3_KI270895v1_alt, chr3_KI270924v1_alt, chr3_KI270934v1_alt, chr3_KI270935v1_alt, chr3_KI270936v1_alt, chr3_KI270937v1_alt, chr3_KN196475v1_fix, chr3_KN196476v1_fix, chr3_KN538364v1_fix, chr3_KQ031385v1_fix, chr3_KQ031386v1_fix, chr3_KV766192v1_fix, chr3_KZ208909v1_alt, chr3_KZ559101v1_alt, chr3_KZ559102v1_alt, chr3_KZ559103v1_alt, chr3_KZ559104v1_fix, chr3_KZ559105v1_alt, chr3_ML143343v1_alt, chr4_GL000008v2_random, chr4_GL000257v2_alt, chr4_GL383528v1_alt, chr4_KI270785v1_alt, chr4_KI270786v1_alt, chr4_KI270787v1_alt, chr4_KI270788v1_alt, chr4_KI270789v1_alt, chr4_KI270790v1_alt, chr4_KI270896v1_alt, chr4_KI270925v1_alt, chr4_KQ090013v1_alt, chr4_KQ090014v1_alt, chr4_KQ090015v1_alt, chr4_KQ983257v1_fix, chr4_KQ983258v1_alt, chr4_KV766193v1_alt, chr4_ML143344v1_fix, chr4_ML143345v1_fix, chr4_ML143346v1_fix, chr4_ML143347v1_fix, chr4_ML143348v1_fix, chr4_ML143349v1_fix, chr5_GL000208v1_random, chr5_GL383530v1_alt, chr5_GL383531v1_alt, chr5_GL383532v1_alt, chr5_GL949742v1_alt, chr5_KI270791v1_alt, chr5_KI270792v1_alt, chr5_KI270793v1_alt, chr5_KI270794v1_alt, chr5_KI270795v1_alt, chr5_KI270796v1_alt, chr5_KI270897v1_alt, chr5_KI270898v1_alt, chr5_KN196477v1_alt, chr5_KV575243v1_alt, chr5_KV575244v1_fix, chr5_KZ208910v1_alt, chr5_ML143350v1_fix, chr6_GL000250v2_alt, chr6_GL000252v2_alt, chr6_GL000253v2_alt, chr6_GL000254v2_alt, chr6_GL000255v2_alt, chr6_GL000256v2_alt, chr6_GL383533v1_alt, chr6_KB021644v2_alt, chr6_KI270758v1_alt, chr6_KI270797v1_alt, chr6_KI270799v1_alt, chr6_KI270800v1_alt, chr6_KI270801v1_alt, chr6_KI270802v1_alt, chr6_KN196478v1_fix, chr6_KQ031387v1_fix, chr6_KQ090016v1_fix, chr6_KQ090017v1_alt, chr6_KV766194v1_fix, chr6_KZ208911v1_fix, chr6_ML143351v1_fix, chr7_GL383534v2_alt, chr7_KI270805v1_alt, chr7_KI270806v1_alt, chr7_KI270807v1_alt, chr7_KI270808v1_alt, chr7_KI270809v1_alt, chr7_KI270899v1_alt, chr7_KQ031388v1_fix, chr7_KV880764v1_fix, chr7_KV880765v1_fix, chr7_KZ208912v1_fix, chr7_KZ208913v1_alt, chr7_KZ559106v1_alt, chr7_ML143352v1_fix, chr8_KI270810v1_alt, chr8_KI270811v1_alt, chr8_KI270812v1_alt, chr8_KI270814v1_alt, chr8_KI270815v1_alt, chr8_KI270816v1_alt, chr8_KI270817v1_alt, chr8_KI270818v1_alt, chr8_KI270819v1_alt, chr8_KI270820v1_alt, chr8_KI270822v1_alt, chr8_KI270900v1_alt, chr8_KI270901v1_alt, chr8_KI270926v1_alt, chr8_KV880766v1_fix, chr8_KV880767v1_fix, chr8_KZ208914v1_fix, chr8_KZ208915v1_fix, chr8_KZ559107v1_alt, chr9_GL383540v1_alt, chr9_GL383541v1_alt, chr9_GL383542v1_alt, chr9_KI270717v1_random, chr9_KI270718v1_random, chr9_KI270719v1_random, chr9_KI270720v1_random, chr9_KI270823v1_alt, chr9_KN196479v1_fix, chr9_KQ090018v1_alt, chr9_KQ090019v1_alt, chr9_ML143353v1_fix, chr10_GL383545v1_alt, chr10_GL383546v1_alt, chr10_KI270824v1_alt, chr10_KI270825v1_alt, chr10_KN196480v1_fix, chr10_KN538365v1_fix, chr10_KN538366v1_fix, chr10_KN538367v1_fix, chr10_KQ090020v1_alt, chr10_KQ090021v1_fix, chr10_ML143354v1_fix, chr10_ML143355v1_fix, chr11_GL383547v1_alt, chr11_JH159136v1_alt, chr11_JH159137v1_alt, chr11_KI270721v1_random, chr11_KI270826v1_alt, chr11_KI270827v1_alt, chr11_KI270829v1_alt, chr11_KI270831v1_alt, chr11_KI270832v1_alt, chr11_KI270902v1_alt, chr11_KI270903v1_alt, chr11_KI270927v1_alt, chr11_KN196481v1_fix, chr11_KN538368v1_alt, chr11_KQ090022v1_fix, chr11_KQ759759v1_fix, chr11_KV766195v1_fix, chr11_KZ559108v1_fix, chr11_KZ559109v1_fix, chr11_KZ559110v1_alt, chr11_KZ559111v1_alt, chr11_ML143356v1_fix, chr11_ML143357v1_fix, chr11_ML143358v1_fix, chr11_ML143359v1_fix, chr11_ML143360v1_fix, chr12_GL383549v1_alt, chr12_GL383550v2_alt, chr12_GL383551v1_alt, chr12_GL383552v1_alt, chr12_GL877875v1_alt, chr12_GL877876v1_alt, chr12_KI270833v1_alt, chr12_KI270834v1_alt, chr12_KI270835v1_alt, chr12_KI270836v1_alt, chr12_KI270837v1_alt, chr12_KI270904v1_alt, chr12_KN196482v1_fix, chr12_KN538369v1_fix, chr12_KN538370v1_fix, chr12_KQ090023v1_alt, chr12_KQ759760v1_fix, chr12_KZ208916v1_fix, chr12_KZ208917v1_fix, chr12_KZ208918v1_alt, chr12_KZ559112v1_alt, chr12_ML143361v1_fix, chr12_ML143362v1_fix, chr13_KI270838v1_alt, chr13_KI270839v1_alt, chr13_KI270840v1_alt, chr13_KI270841v1_alt, chr13_KI270842v1_alt, chr13_KI270843v1_alt, chr13_KN196483v1_fix, chr13_KN538371v1_fix, chr13_KN538372v1_fix, chr13_KN538373v1_fix, chr13_KQ090024v1_alt, chr13_KQ090025v1_alt, chr13_ML143363v1_fix, chr13_ML143364v1_fix, chr13_ML143365v1_fix, chr13_ML143366v1_fix, chr14_GL000009v2_random, chr14_GL000194v1_random, chr14_KI270722v1_random, chr14_KI270723v1_random, chr14_KI270724v1_random, chr14_KI270725v1_random, chr14_KI270726v1_random, chr14_KI270844v1_alt, chr14_KI270845v1_alt, chr14_KI270846v1_alt, chr14_KI270847v1_alt, chr14_KZ208919v1_alt, chr14_KZ208920v1_fix, chr14_ML143367v1_fix, chr14_ML143368v1_alt, chr15_GL383554v1_alt, chr15_GL383555v2_alt, chr15_KI270727v1_random, chr15_KI270848v1_alt, chr15_KI270849v1_alt, chr15_KI270851v1_alt, chr15_KI270852v1_alt, chr15_KI270906v1_alt, chr15_KN538374v1_fix, chr15_KQ031389v1_alt, chr15_ML143369v1_fix, chr15_ML143370v1_fix, chr15_ML143371v1_fix, chr15_ML143372v1_fix, chr16_GL383556v1_alt, chr16_GL383557v1_alt, chr16_KI270728v1_random, chr16_KI270854v1_alt, chr16_KI270855v1_alt, chr16_KI270856v1_alt, chr16_KQ031390v1_alt, chr16_KQ090026v1_alt, chr16_KQ090027v1_alt, chr16_KV880768v1_fix, chr16_KZ208921v1_alt, chr16_KZ559113v1_fix, chr16_ML143373v1_fix, chr17_GL000258v2_alt, chr17_GL383563v3_alt, chr17_GL383564v2_alt, chr17_GL383565v1_alt, chr17_GL383566v1_alt, chr17_JH159146v1_alt, chr17_JH159147v1_alt, chr17_JH159148v1_alt, chr17_KI270730v1_random, chr17_KI270857v1_alt, chr17_KI270858v1_alt, chr17_KI270859v1_alt, chr17_KI270860v1_alt, chr17_KI270861v1_alt, chr17_KI270862v1_alt, chr17_KI270907v1_alt, chr17_KI270908v1_alt, chr17_KI270909v1_alt, chr17_KI270910v1_alt, chr17_KV575245v1_fix, chr17_KV766196v1_fix, chr17_KV766197v1_alt, chr17_KV766198v1_alt, chr17_KZ559114v1_alt, chr17_ML143374v1_fix, chr17_ML143375v1_fix, chr18_GL383567v1_alt, chr18_GL383568v1_alt, chr18_GL383569v1_alt, chr18_GL383570v1_alt, chr18_GL383571v1_alt, chr18_GL383572v1_alt, chr18_KI270863v1_alt, chr18_KI270864v1_alt, chr18_KI270911v1_alt, chr18_KI270912v1

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': JTFH01000247.1, JTFH01000515.1, JTFH01000804.1, JTFH01000876.1, JTFH01001024.1, JTFH01001390.1, JTFH01001405.1, JTFH01001430.1, JTFH01001465.1, JTFH01001478.1, JTFH01001512.1, JTFH01001549.1, JTFH01001680.1, JTFH01001724.1, JTFH01001862.1, JTFH01001929.1, JTFH01001959.1, JTFH01001981.1, JTFH01001998.1, KN707720.1, KN707809.1, KN707828.1, KN707893.1, KN707896.1, JTFH01000028.1, JTFH01000280.1, JTFH01000942.1, JTFH01001023.1, JTFH01001317.1, JTFH01001613.1, JTFH01001899.1, KN707626.1
##   - in 'y': chrM, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270706v1_random, chr1_KI270707v1_random, chr1_KI270708v1_random, chr1_KI270709v1_random, chr1_KI270710v1_random, chr1_KI270711v1_random, chr1_KI270712v1_random, chr1_KI270714v1_random, chr1_KI270759v1_alt, chr1_KI270760v1_alt, chr1_KI270761v1_alt, chr1_KI270762v1_alt, chr1_KI270763v1_alt, chr1_KI270764v1_alt, chr1_KI270765v1_alt, chr1_KI270766v1_alt, chr1_KI270892v1_alt, chr1_KN196472v1_fix, chr1_KN196473v1_fix, chr1_KN196474v1_fix, chr1_KN538360v1_fix, chr1_KN538361v1_fix, chr1_KQ031383v1_fix, chr1_KQ458382v1_alt, chr1_KQ458383v1_alt, chr1_KQ458384v1_alt, chr1_KQ983255v1_alt, chr1_KV880763v1_alt, chr1_KZ208904v1_alt, chr1_KZ208905v1_alt, chr1_KZ208906v1_fix, chr1_KZ559100v1_fix, chr2_GL383521v1_alt, chr2_GL383522v1_alt, chr2_GL582966v2_alt, chr2_KI270715v1_random, chr2_KI270716v1_random, chr2_KI270767v1_alt, chr2_KI270768v1_alt, chr2_KI270769v1_alt, chr2_KI270770v1_alt, chr2_KI270771v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270775v1_alt, chr2_KI270776v1_alt, chr2_KI270893v1_alt, chr2_KI270894v1_alt, chr2_KN538362v1_fix, chr2_KN538363v1_fix, chr2_KQ031384v1_fix, chr2_KQ983256v1_alt, chr2_KZ208907v1_alt, chr2_KZ208908v1_alt, chr2_ML143341v1_fix, chr2_ML143342v1_fix, chr3_GL000221v1_random, chr3_GL383526v1_alt, chr3_JH636055v2_alt, chr3_KI270777v1_alt, chr3_KI270778v1_alt, chr3_KI270779v1_alt, chr3_KI270780v1_alt, chr3_KI270781v1_alt, chr3_KI270782v1_alt, chr3_KI270783v1_alt, chr3_KI270784v1_alt, chr3_KI270895v1_alt, chr3_KI270924v1_alt, chr3_KI270934v1_alt, chr3_KI270935v1_alt, chr3_KI270936v1_alt, chr3_KI270937v1_alt, chr3_KN196475v1_fix, chr3_KN196476v1_fix, chr3_KN538364v1_fix, chr3_KQ031385v1_fix, chr3_KQ031386v1_fix, chr3_KV766192v1_fix, chr3_KZ208909v1_alt, chr3_KZ559101v1_alt, chr3_KZ559102v1_alt, chr3_KZ559103v1_alt, chr3_KZ559104v1_fix, chr3_KZ559105v1_alt, chr3_ML143343v1_alt, chr4_GL000008v2_random, chr4_GL000257v2_alt, chr4_GL383528v1_alt, chr4_KI270785v1_alt, chr4_KI270786v1_alt, chr4_KI270787v1_alt, chr4_KI270788v1_alt, chr4_KI270789v1_alt, chr4_KI270790v1_alt, chr4_KI270896v1_alt, chr4_KI270925v1_alt, chr4_KQ090013v1_alt, chr4_KQ090014v1_alt, chr4_KQ090015v1_alt, chr4_KQ983257v1_fix, chr4_KQ983258v1_alt, chr4_KV766193v1_alt, chr4_ML143344v1_fix, chr4_ML143345v1_fix, chr4_ML143346v1_fix, chr4_ML143347v1_fix, chr4_ML143348v1_fix, chr4_ML143349v1_fix, chr5_GL000208v1_random, chr5_GL383530v1_alt, chr5_GL383531v1_alt, chr5_GL383532v1_alt, chr5_GL949742v1_alt, chr5_KI270791v1_alt, chr5_KI270792v1_alt, chr5_KI270793v1_alt, chr5_KI270794v1_alt, chr5_KI270795v1_alt, chr5_KI270796v1_alt, chr5_KI270897v1_alt, chr5_KI270898v1_alt, chr5_KN196477v1_alt, chr5_KV575243v1_alt, chr5_KV575244v1_fix, chr5_KZ208910v1_alt, chr5_ML143350v1_fix, chr6_GL000250v2_alt, chr6_GL000252v2_alt, chr6_GL000253v2_alt, chr6_GL000254v2_alt, chr6_GL000255v2_alt, chr6_GL000256v2_alt, chr6_GL383533v1_alt, chr6_KB021644v2_alt, chr6_KI270758v1_alt, chr6_KI270797v1_alt, chr6_KI270799v1_alt, chr6_KI270800v1_alt, chr6_KI270801v1_alt, chr6_KI270802v1_alt, chr6_KN196478v1_fix, chr6_KQ031387v1_fix, chr6_KQ090016v1_fix, chr6_KQ090017v1_alt, chr6_KV766194v1_fix, chr6_KZ208911v1_fix, chr6_ML143351v1_fix, chr7_GL383534v2_alt, chr7_KI270805v1_alt, chr7_KI270806v1_alt, chr7_KI270807v1_alt, chr7_KI270808v1_alt, chr7_KI270809v1_alt, chr7_KI270899v1_alt, chr7_KQ031388v1_fix, chr7_KV880764v1_fix, chr7_KV880765v1_fix, chr7_KZ208912v1_fix, chr7_KZ208913v1_alt, chr7_KZ559106v1_alt, chr7_ML143352v1_fix, chr8_KI270810v1_alt, chr8_KI270811v1_alt, chr8_KI270812v1_alt, chr8_KI270814v1_alt, chr8_KI270815v1_alt, chr8_KI270816v1_alt, chr8_KI270817v1_alt, chr8_KI270818v1_alt, chr8_KI270819v1_alt, chr8_KI270820v1_alt, chr8_KI270822v1_alt, chr8_KI270900v1_alt, chr8_KI270901v1_alt, chr8_KI270926v1_alt, chr8_KV880766v1_fix, chr8_KV880767v1_fix, chr8_KZ208914v1_fix, chr8_KZ208915v1_fix, chr8_KZ559107v1_alt, chr9_GL383540v1_alt, chr9_GL383541v1_alt, chr9_GL383542v1_alt, chr9_KI270717v1_random, chr9_KI270718v1_random, chr9_KI270719v1_random, chr9_KI270720v1_random, chr9_KI270823v1_alt, chr9_KN196479v1_fix, chr9_KQ090018v1_alt, chr9_KQ090019v1_alt, chr9_ML143353v1_fix, chr10_GL383545v1_alt, chr10_GL383546v1_alt, chr10_KI270824v1_alt, chr10_KI270825v1_alt, chr10_KN196480v1_fix, chr10_KN538365v1_fix, chr10_KN538366v1_fix, chr10_KN538367v1_fix, chr10_KQ090020v1_alt, chr10_KQ090021v1_fix, chr10_ML143354v1_fix, chr10_ML143355v1_fix, chr11_GL383547v1_alt, chr11_JH159136v1_alt, chr11_JH159137v1_alt, chr11_KI270721v1_random, chr11_KI270826v1_alt, chr11_KI270827v1_alt, chr11_KI270829v1_alt, chr11_KI270831v1_alt, chr11_KI270832v1_alt, chr11_KI270902v1_alt, chr11_KI270903v1_alt, chr11_KI270927v1_alt, chr11_KN196481v1_fix, chr11_KN538368v1_alt, chr11_KQ090022v1_fix, chr11_KQ759759v1_fix, chr11_KV766195v1_fix, chr11_KZ559108v1_fix, chr11_KZ559109v1_fix, chr11_KZ559110v1_alt, chr11_KZ559111v1_alt, chr11_ML143356v1_fix, chr11_ML143357v1_fix, chr11_ML143358v1_fix, chr11_ML143359v1_fix, chr11_ML143360v1_fix, chr12_GL383549v1_alt, chr12_GL383550v2_alt, chr12_GL383551v1_alt, chr12_GL383552v1_alt, chr12_GL877875v1_alt, chr12_GL877876v1_alt, chr12_KI270833v1_alt, chr12_KI270834v1_alt, chr12_KI270835v1_alt, chr12_KI270836v1_alt, chr12_KI270837v1_alt, chr12_KI270904v1_alt, chr12_KN196482v1_fix, chr12_KN538369v1_fix, chr12_KN538370v1_fix, chr12_KQ090023v1_alt, chr12_KQ759760v1_fix, chr12_KZ208916v1_fix, chr12_KZ208917v1_fix, chr12_KZ208918v1_alt, chr12_KZ559112v1_alt, chr12_ML143361v1_fix, chr12_ML143362v1_fix, chr13_KI270838v1_alt, chr13_KI270839v1_alt, chr13_KI270840v1_alt, chr13_KI270841v1_alt, chr13_KI270842v1_alt, chr13_KI270843v1_alt, chr13_KN196483v1_fix, chr13_KN538371v1_fix, chr13_KN538372v1_fix, chr13_KN538373v1_fix, chr13_KQ090024v1_alt, chr13_KQ090025v1_alt, chr13_ML143363v1_fix, chr13_ML143364v1_fix, chr13_ML143365v1_fix, chr13_ML143366v1_fix, chr14_GL000009v2_random, chr14_GL000194v1_random, chr14_KI270722v1_random, chr14_KI270723v1_random, chr14_KI270724v1_random, chr14_KI270725v1_random, chr14_KI270726v1_random, chr14_KI270844v1_alt, chr14_KI270845v1_alt, chr14_KI270846v1_alt, chr14_KI270847v1_alt, chr14_KZ208919v1_alt, chr14_KZ208920v1_fix, chr14_ML143367v1_fix, chr14_ML143368v1_alt, chr15_GL383554v1_alt, chr15_GL383555v2_alt, chr15_KI270727v1_random, chr15_KI270848v1_alt, chr15_KI270849v1_alt, chr15_KI270851v1_alt, chr15_KI270852v1_alt, chr15_KI270906v1_alt, chr15_KN538374v1_fix, chr15_KQ031389v1_alt, chr15_ML143369v1_fix, chr15_ML143370v1_fix, chr15_ML143371v1_fix, chr15_ML143372v1_fix, chr16_GL383556v1_alt, chr16_GL383557v1_alt, chr16_KI270728v1_random, chr16_KI270854v1_alt, chr16_KI270855v1_alt, chr16_KI270856v1_alt, chr16_KQ031390v1_alt, chr16_KQ090026v1_alt, chr16_KQ090027v1_alt, chr16_KV880768v1_fix, chr16_KZ208921v1_alt, chr16_KZ559113v1_fix, chr16_ML143373v1_fix, chr17_GL000258v2_alt, chr17_GL383563v3_alt, chr17_GL383564v2_alt, chr17_GL383565v1_alt, chr17_GL383566v1_alt, chr17_JH159146v1_alt, chr17_JH159147v1_alt, chr17_JH159148v1_alt, chr17_KI270730v1_random, chr17_KI270857v1_alt, chr17_KI270858v1_alt, chr17_KI270859v1_alt, chr17_KI270860v1_alt, chr17_KI270861v1_alt, chr17_KI270862v1_alt, chr17_KI270907v1_alt, chr17_KI270908v1_alt, chr17_KI270909v1_alt, chr17_KI270910v1_alt, chr17_KV575245v1_fix, chr17_KV766196v1_fix, chr17_KV766197v1_alt, chr17_KV766198v1_alt, chr17_KZ559114v1_alt, chr17_ML143374v1_fix, chr17_ML143375v1_fix, chr18_GL383567v1_alt, chr18_GL383568v1_alt, chr18_GL383569v1_alt, chr18_GL383570v1_alt, chr18_GL383571v1_alt, chr18_GL383572v1_alt, chr18_KI270863v1_alt, chr18_KI270864v1_alt, chr18_KI270911v1_alt, chr18_KI270912v1

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': JTFH01000247.1, JTFH01000515.1, JTFH01000804.1, JTFH01000876.1, JTFH01001024.1, JTFH01001390.1, JTFH01001405.1, JTFH01001430.1, JTFH01001465.1, JTFH01001478.1, JTFH01001512.1, JTFH01001549.1, JTFH01001680.1, JTFH01001724.1, JTFH01001862.1, JTFH01001929.1, JTFH01001959.1, JTFH01001981.1, JTFH01001998.1, KN707720.1, KN707809.1, KN707828.1, KN707893.1, KN707896.1, JTFH01000028.1, JTFH01000280.1, JTFH01000942.1, JTFH01001023.1, JTFH01001317.1, JTFH01001613.1, JTFH01001899.1, KN707626.1
##   - in 'y': chrM, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270706v1_random, chr1_KI270707v1_random, chr1_KI270708v1_random, chr1_KI270709v1_random, chr1_KI270710v1_random, chr1_KI270711v1_random, chr1_KI270712v1_random, chr1_KI270714v1_random, chr1_KI270759v1_alt, chr1_KI270760v1_alt, chr1_KI270761v1_alt, chr1_KI270762v1_alt, chr1_KI270763v1_alt, chr1_KI270764v1_alt, chr1_KI270765v1_alt, chr1_KI270766v1_alt, chr1_KI270892v1_alt, chr1_KN196472v1_fix, chr1_KN196473v1_fix, chr1_KN196474v1_fix, chr1_KN538360v1_fix, chr1_KN538361v1_fix, chr1_KQ031383v1_fix, chr1_KQ458382v1_alt, chr1_KQ458383v1_alt, chr1_KQ458384v1_alt, chr1_KQ983255v1_alt, chr1_KV880763v1_alt, chr1_KZ208904v1_alt, chr1_KZ208905v1_alt, chr1_KZ208906v1_fix, chr1_KZ559100v1_fix, chr2_GL383521v1_alt, chr2_GL383522v1_alt, chr2_GL582966v2_alt, chr2_KI270715v1_random, chr2_KI270716v1_random, chr2_KI270767v1_alt, chr2_KI270768v1_alt, chr2_KI270769v1_alt, chr2_KI270770v1_alt, chr2_KI270771v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270775v1_alt, chr2_KI270776v1_alt, chr2_KI270893v1_alt, chr2_KI270894v1_alt, chr2_KN538362v1_fix, chr2_KN538363v1_fix, chr2_KQ031384v1_fix, chr2_KQ983256v1_alt, chr2_KZ208907v1_alt, chr2_KZ208908v1_alt, chr2_ML143341v1_fix, chr2_ML143342v1_fix, chr3_GL000221v1_random, chr3_GL383526v1_alt, chr3_JH636055v2_alt, chr3_KI270777v1_alt, chr3_KI270778v1_alt, chr3_KI270779v1_alt, chr3_KI270780v1_alt, chr3_KI270781v1_alt, chr3_KI270782v1_alt, chr3_KI270783v1_alt, chr3_KI270784v1_alt, chr3_KI270895v1_alt, chr3_KI270924v1_alt, chr3_KI270934v1_alt, chr3_KI270935v1_alt, chr3_KI270936v1_alt, chr3_KI270937v1_alt, chr3_KN196475v1_fix, chr3_KN196476v1_fix, chr3_KN538364v1_fix, chr3_KQ031385v1_fix, chr3_KQ031386v1_fix, chr3_KV766192v1_fix, chr3_KZ208909v1_alt, chr3_KZ559101v1_alt, chr3_KZ559102v1_alt, chr3_KZ559103v1_alt, chr3_KZ559104v1_fix, chr3_KZ559105v1_alt, chr3_ML143343v1_alt, chr4_GL000008v2_random, chr4_GL000257v2_alt, chr4_GL383528v1_alt, chr4_KI270785v1_alt, chr4_KI270786v1_alt, chr4_KI270787v1_alt, chr4_KI270788v1_alt, chr4_KI270789v1_alt, chr4_KI270790v1_alt, chr4_KI270896v1_alt, chr4_KI270925v1_alt, chr4_KQ090013v1_alt, chr4_KQ090014v1_alt, chr4_KQ090015v1_alt, chr4_KQ983257v1_fix, chr4_KQ983258v1_alt, chr4_KV766193v1_alt, chr4_ML143344v1_fix, chr4_ML143345v1_fix, chr4_ML143346v1_fix, chr4_ML143347v1_fix, chr4_ML143348v1_fix, chr4_ML143349v1_fix, chr5_GL000208v1_random, chr5_GL383530v1_alt, chr5_GL383531v1_alt, chr5_GL383532v1_alt, chr5_GL949742v1_alt, chr5_KI270791v1_alt, chr5_KI270792v1_alt, chr5_KI270793v1_alt, chr5_KI270794v1_alt, chr5_KI270795v1_alt, chr5_KI270796v1_alt, chr5_KI270897v1_alt, chr5_KI270898v1_alt, chr5_KN196477v1_alt, chr5_KV575243v1_alt, chr5_KV575244v1_fix, chr5_KZ208910v1_alt, chr5_ML143350v1_fix, chr6_GL000250v2_alt, chr6_GL000252v2_alt, chr6_GL000253v2_alt, chr6_GL000254v2_alt, chr6_GL000255v2_alt, chr6_GL000256v2_alt, chr6_GL383533v1_alt, chr6_KB021644v2_alt, chr6_KI270758v1_alt, chr6_KI270797v1_alt, chr6_KI270799v1_alt, chr6_KI270800v1_alt, chr6_KI270801v1_alt, chr6_KI270802v1_alt, chr6_KN196478v1_fix, chr6_KQ031387v1_fix, chr6_KQ090016v1_fix, chr6_KQ090017v1_alt, chr6_KV766194v1_fix, chr6_KZ208911v1_fix, chr6_ML143351v1_fix, chr7_GL383534v2_alt, chr7_KI270805v1_alt, chr7_KI270806v1_alt, chr7_KI270807v1_alt, chr7_KI270808v1_alt, chr7_KI270809v1_alt, chr7_KI270899v1_alt, chr7_KQ031388v1_fix, chr7_KV880764v1_fix, chr7_KV880765v1_fix, chr7_KZ208912v1_fix, chr7_KZ208913v1_alt, chr7_KZ559106v1_alt, chr7_ML143352v1_fix, chr8_KI270810v1_alt, chr8_KI270811v1_alt, chr8_KI270812v1_alt, chr8_KI270814v1_alt, chr8_KI270815v1_alt, chr8_KI270816v1_alt, chr8_KI270817v1_alt, chr8_KI270818v1_alt, chr8_KI270819v1_alt, chr8_KI270820v1_alt, chr8_KI270822v1_alt, chr8_KI270900v1_alt, chr8_KI270901v1_alt, chr8_KI270926v1_alt, chr8_KV880766v1_fix, chr8_KV880767v1_fix, chr8_KZ208914v1_fix, chr8_KZ208915v1_fix, chr8_KZ559107v1_alt, chr9_GL383540v1_alt, chr9_GL383541v1_alt, chr9_GL383542v1_alt, chr9_KI270717v1_random, chr9_KI270718v1_random, chr9_KI270719v1_random, chr9_KI270720v1_random, chr9_KI270823v1_alt, chr9_KN196479v1_fix, chr9_KQ090018v1_alt, chr9_KQ090019v1_alt, chr9_ML143353v1_fix, chr10_GL383545v1_alt, chr10_GL383546v1_alt, chr10_KI270824v1_alt, chr10_KI270825v1_alt, chr10_KN196480v1_fix, chr10_KN538365v1_fix, chr10_KN538366v1_fix, chr10_KN538367v1_fix, chr10_KQ090020v1_alt, chr10_KQ090021v1_fix, chr10_ML143354v1_fix, chr10_ML143355v1_fix, chr11_GL383547v1_alt, chr11_JH159136v1_alt, chr11_JH159137v1_alt, chr11_KI270721v1_random, chr11_KI270826v1_alt, chr11_KI270827v1_alt, chr11_KI270829v1_alt, chr11_KI270831v1_alt, chr11_KI270832v1_alt, chr11_KI270902v1_alt, chr11_KI270903v1_alt, chr11_KI270927v1_alt, chr11_KN196481v1_fix, chr11_KN538368v1_alt, chr11_KQ090022v1_fix, chr11_KQ759759v1_fix, chr11_KV766195v1_fix, chr11_KZ559108v1_fix, chr11_KZ559109v1_fix, chr11_KZ559110v1_alt, chr11_KZ559111v1_alt, chr11_ML143356v1_fix, chr11_ML143357v1_fix, chr11_ML143358v1_fix, chr11_ML143359v1_fix, chr11_ML143360v1_fix, chr12_GL383549v1_alt, chr12_GL383550v2_alt, chr12_GL383551v1_alt, chr12_GL383552v1_alt, chr12_GL877875v1_alt, chr12_GL877876v1_alt, chr12_KI270833v1_alt, chr12_KI270834v1_alt, chr12_KI270835v1_alt, chr12_KI270836v1_alt, chr12_KI270837v1_alt, chr12_KI270904v1_alt, chr12_KN196482v1_fix, chr12_KN538369v1_fix, chr12_KN538370v1_fix, chr12_KQ090023v1_alt, chr12_KQ759760v1_fix, chr12_KZ208916v1_fix, chr12_KZ208917v1_fix, chr12_KZ208918v1_alt, chr12_KZ559112v1_alt, chr12_ML143361v1_fix, chr12_ML143362v1_fix, chr13_KI270838v1_alt, chr13_KI270839v1_alt, chr13_KI270840v1_alt, chr13_KI270841v1_alt, chr13_KI270842v1_alt, chr13_KI270843v1_alt, chr13_KN196483v1_fix, chr13_KN538371v1_fix, chr13_KN538372v1_fix, chr13_KN538373v1_fix, chr13_KQ090024v1_alt, chr13_KQ090025v1_alt, chr13_ML143363v1_fix, chr13_ML143364v1_fix, chr13_ML143365v1_fix, chr13_ML143366v1_fix, chr14_GL000009v2_random, chr14_GL000194v1_random, chr14_KI270722v1_random, chr14_KI270723v1_random, chr14_KI270724v1_random, chr14_KI270725v1_random, chr14_KI270726v1_random, chr14_KI270844v1_alt, chr14_KI270845v1_alt, chr14_KI270846v1_alt, chr14_KI270847v1_alt, chr14_KZ208919v1_alt, chr14_KZ208920v1_fix, chr14_ML143367v1_fix, chr14_ML143368v1_alt, chr15_GL383554v1_alt, chr15_GL383555v2_alt, chr15_KI270727v1_random, chr15_KI270848v1_alt, chr15_KI270849v1_alt, chr15_KI270851v1_alt, chr15_KI270852v1_alt, chr15_KI270906v1_alt, chr15_KN538374v1_fix, chr15_KQ031389v1_alt, chr15_ML143369v1_fix, chr15_ML143370v1_fix, chr15_ML143371v1_fix, chr15_ML143372v1_fix, chr16_GL383556v1_alt, chr16_GL383557v1_alt, chr16_KI270728v1_random, chr16_KI270854v1_alt, chr16_KI270855v1_alt, chr16_KI270856v1_alt, chr16_KQ031390v1_alt, chr16_KQ090026v1_alt, chr16_KQ090027v1_alt, chr16_KV880768v1_fix, chr16_KZ208921v1_alt, chr16_KZ559113v1_fix, chr16_ML143373v1_fix, chr17_GL000258v2_alt, chr17_GL383563v3_alt, chr17_GL383564v2_alt, chr17_GL383565v1_alt, chr17_GL383566v1_alt, chr17_JH159146v1_alt, chr17_JH159147v1_alt, chr17_JH159148v1_alt, chr17_KI270730v1_random, chr17_KI270857v1_alt, chr17_KI270858v1_alt, chr17_KI270859v1_alt, chr17_KI270860v1_alt, chr17_KI270861v1_alt, chr17_KI270862v1_alt, chr17_KI270907v1_alt, chr17_KI270908v1_alt, chr17_KI270909v1_alt, chr17_KI270910v1_alt, chr17_KV575245v1_fix, chr17_KV766196v1_fix, chr17_KV766197v1_alt, chr17_KV766198v1_alt, chr17_KZ559114v1_alt, chr17_ML143374v1_fix, chr17_ML143375v1_fix, chr18_GL383567v1_alt, chr18_GL383568v1_alt, chr18_GL383569v1_alt, chr18_GL383570v1_alt, chr18_GL383571v1_alt, chr18_GL383572v1_alt, chr18_KI270863v1_alt, chr18_KI270864v1_alt, chr18_KI270911v1_alt, chr18_KI270912v1

## >> adding gene annotation...          2022-04-20 11:23:00

## 'select()' returned 1:1 mapping between keys and columns

## >> assigning chromosome lengths           2022-04-20 11:23:00 
## >> done...                    2022-04-20 11:23:00

res.lfcShrink.granges.ChIPseeker.background <- annotatePeak(res.lfcShrink.granges[res.lfcShrink.granges$padj >
    0.05], tssRegion = c(-5000, 5000), flankDistance = 5000,
    TxDb = TxDb.Hsapiens.UCSC.hg38.knownGene, annoDb = "org.Hs.eg.db",
    overlap = "TSS", level = "gene")

## >> preparing features information...      2022-04-20 11:23:00 
## >> identifying nearest features...        2022-04-20 11:23:00

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': JTFH01000247.1, JTFH01000515.1, JTFH01000804.1, JTFH01000876.1, JTFH01001024.1, JTFH01001390.1, JTFH01001405.1, JTFH01001430.1, JTFH01001465.1, JTFH01001478.1, JTFH01001512.1, JTFH01001549.1, JTFH01001680.1, JTFH01001724.1, JTFH01001862.1, JTFH01001929.1, JTFH01001959.1, JTFH01001981.1, JTFH01001998.1, KN707720.1, KN707809.1, KN707828.1, KN707893.1, KN707896.1, JTFH01000028.1, JTFH01000280.1, JTFH01000942.1, JTFH01001023.1, JTFH01001317.1, JTFH01001613.1, JTFH01001899.1, KN707626.1
##   - in 'y': chrM, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270706v1_random, chr1_KI270707v1_random, chr1_KI270708v1_random, chr1_KI270709v1_random, chr1_KI270710v1_random, chr1_KI270711v1_random, chr1_KI270712v1_random, chr1_KI270714v1_random, chr1_KI270759v1_alt, chr1_KI270760v1_alt, chr1_KI270761v1_alt, chr1_KI270762v1_alt, chr1_KI270763v1_alt, chr1_KI270764v1_alt, chr1_KI270765v1_alt, chr1_KI270766v1_alt, chr1_KI270892v1_alt, chr1_KN196472v1_fix, chr1_KN196473v1_fix, chr1_KN196474v1_fix, chr1_KN538360v1_fix, chr1_KN538361v1_fix, chr1_KQ031383v1_fix, chr1_KQ458382v1_alt, chr1_KQ458383v1_alt, chr1_KQ458384v1_alt, chr1_KQ983255v1_alt, chr1_KV880763v1_alt, chr1_KZ208904v1_alt, chr1_KZ208905v1_alt, chr1_KZ208906v1_fix, chr1_KZ559100v1_fix, chr2_GL383521v1_alt, chr2_GL383522v1_alt, chr2_GL582966v2_alt, chr2_KI270715v1_random, chr2_KI270716v1_random, chr2_KI270767v1_alt, chr2_KI270768v1_alt, chr2_KI270769v1_alt, chr2_KI270770v1_alt, chr2_KI270771v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270775v1_alt, chr2_KI270776v1_alt, chr2_KI270893v1_alt, chr2_KI270894v1_alt, chr2_KN538362v1_fix, chr2_KN538363v1_fix, chr2_KQ031384v1_fix, chr2_KQ983256v1_alt, chr2_KZ208907v1_alt, chr2_KZ208908v1_alt, chr2_ML143341v1_fix, chr2_ML143342v1_fix, chr3_GL000221v1_random, chr3_GL383526v1_alt, chr3_JH636055v2_alt, chr3_KI270777v1_alt, chr3_KI270778v1_alt, chr3_KI270779v1_alt, chr3_KI270780v1_alt, chr3_KI270781v1_alt, chr3_KI270782v1_alt, chr3_KI270783v1_alt, chr3_KI270784v1_alt, chr3_KI270895v1_alt, chr3_KI270924v1_alt, chr3_KI270934v1_alt, chr3_KI270935v1_alt, chr3_KI270936v1_alt, chr3_KI270937v1_alt, chr3_KN196475v1_fix, chr3_KN196476v1_fix, chr3_KN538364v1_fix, chr3_KQ031385v1_fix, chr3_KQ031386v1_fix, chr3_KV766192v1_fix, chr3_KZ208909v1_alt, chr3_KZ559101v1_alt, chr3_KZ559102v1_alt, chr3_KZ559103v1_alt, chr3_KZ559104v1_fix, chr3_KZ559105v1_alt, chr3_ML143343v1_alt, chr4_GL000008v2_random, chr4_GL000257v2_alt, chr4_GL383528v1_alt, chr4_KI270785v1_alt, chr4_KI270786v1_alt, chr4_KI270787v1_alt, chr4_KI270788v1_alt, chr4_KI270789v1_alt, chr4_KI270790v1_alt, chr4_KI270896v1_alt, chr4_KI270925v1_alt, chr4_KQ090013v1_alt, chr4_KQ090014v1_alt, chr4_KQ090015v1_alt, chr4_KQ983257v1_fix, chr4_KQ983258v1_alt, chr4_KV766193v1_alt, chr4_ML143344v1_fix, chr4_ML143345v1_fix, chr4_ML143346v1_fix, chr4_ML143347v1_fix, chr4_ML143348v1_fix, chr4_ML143349v1_fix, chr5_GL000208v1_random, chr5_GL383530v1_alt, chr5_GL383531v1_alt, chr5_GL383532v1_alt, chr5_GL949742v1_alt, chr5_KI270791v1_alt, chr5_KI270792v1_alt, chr5_KI270793v1_alt, chr5_KI270794v1_alt, chr5_KI270795v1_alt, chr5_KI270796v1_alt, chr5_KI270897v1_alt, chr5_KI270898v1_alt, chr5_KN196477v1_alt, chr5_KV575243v1_alt, chr5_KV575244v1_fix, chr5_KZ208910v1_alt, chr5_ML143350v1_fix, chr6_GL000250v2_alt, chr6_GL000252v2_alt, chr6_GL000253v2_alt, chr6_GL000254v2_alt, chr6_GL000255v2_alt, chr6_GL000256v2_alt, chr6_GL383533v1_alt, chr6_KB021644v2_alt, chr6_KI270758v1_alt, chr6_KI270797v1_alt, chr6_KI270799v1_alt, chr6_KI270800v1_alt, chr6_KI270801v1_alt, chr6_KI270802v1_alt, chr6_KN196478v1_fix, chr6_KQ031387v1_fix, chr6_KQ090016v1_fix, chr6_KQ090017v1_alt, chr6_KV766194v1_fix, chr6_KZ208911v1_fix, chr6_ML143351v1_fix, chr7_GL383534v2_alt, chr7_KI270805v1_alt, chr7_KI270806v1_alt, chr7_KI270807v1_alt, chr7_KI270808v1_alt, chr7_KI270809v1_alt, chr7_KI270899v1_alt, chr7_KQ031388v1_fix, chr7_KV880764v1_fix, chr7_KV880765v1_fix, chr7_KZ208912v1_fix, chr7_KZ208913v1_alt, chr7_KZ559106v1_alt, chr7_ML143352v1_fix, chr8_KI270810v1_alt, chr8_KI270811v1_alt, chr8_KI270812v1_alt, chr8_KI270814v1_alt, chr8_KI270815v1_alt, chr8_KI270816v1_alt, chr8_KI270817v1_alt, chr8_KI270818v1_alt, chr8_KI270819v1_alt, chr8_KI270820v1_alt, chr8_KI270822v1_alt, chr8_KI270900v1_alt, chr8_KI270901v1_alt, chr8_KI270926v1_alt, chr8_KV880766v1_fix, chr8_KV880767v1_fix, chr8_KZ208914v1_fix, chr8_KZ208915v1_fix, chr8_KZ559107v1_alt, chr9_GL383540v1_alt, chr9_GL383541v1_alt, chr9_GL383542v1_alt, chr9_KI270717v1_random, chr9_KI270718v1_random, chr9_KI270719v1_random, chr9_KI270720v1_random, chr9_KI270823v1_alt, chr9_KN196479v1_fix, chr9_KQ090018v1_alt, chr9_KQ090019v1_alt, chr9_ML143353v1_fix, chr10_GL383545v1_alt, chr10_GL383546v1_alt, chr10_KI270824v1_alt, chr10_KI270825v1_alt, chr10_KN196480v1_fix, chr10_KN538365v1_fix, chr10_KN538366v1_fix, chr10_KN538367v1_fix, chr10_KQ090020v1_alt, chr10_KQ090021v1_fix, chr10_ML143354v1_fix, chr10_ML143355v1_fix, chr11_GL383547v1_alt, chr11_JH159136v1_alt, chr11_JH159137v1_alt, chr11_KI270721v1_random, chr11_KI270826v1_alt, chr11_KI270827v1_alt, chr11_KI270829v1_alt, chr11_KI270831v1_alt, chr11_KI270832v1_alt, chr11_KI270902v1_alt, chr11_KI270903v1_alt, chr11_KI270927v1_alt, chr11_KN196481v1_fix, chr11_KN538368v1_alt, chr11_KQ090022v1_fix, chr11_KQ759759v1_fix, chr11_KV766195v1_fix, chr11_KZ559108v1_fix, chr11_KZ559109v1_fix, chr11_KZ559110v1_alt, chr11_KZ559111v1_alt, chr11_ML143356v1_fix, chr11_ML143357v1_fix, chr11_ML143358v1_fix, chr11_ML143359v1_fix, chr11_ML143360v1_fix, chr12_GL383549v1_alt, chr12_GL383550v2_alt, chr12_GL383551v1_alt, chr12_GL383552v1_alt, chr12_GL877875v1_alt, chr12_GL877876v1_alt, chr12_KI270833v1_alt, chr12_KI270834v1_alt, chr12_KI270835v1_alt, chr12_KI270836v1_alt, chr12_KI270837v1_alt, chr12_KI270904v1_alt, chr12_KN196482v1_fix, chr12_KN538369v1_fix, chr12_KN538370v1_fix, chr12_KQ090023v1_alt, chr12_KQ759760v1_fix, chr12_KZ208916v1_fix, chr12_KZ208917v1_fix, chr12_KZ208918v1_alt, chr12_KZ559112v1_alt, chr12_ML143361v1_fix, chr12_ML143362v1_fix, chr13_KI270838v1_alt, chr13_KI270839v1_alt, chr13_KI270840v1_alt, chr13_KI270841v1_alt, chr13_KI270842v1_alt, chr13_KI270843v1_alt, chr13_KN196483v1_fix, chr13_KN538371v1_fix, chr13_KN538372v1_fix, chr13_KN538373v1_fix, chr13_KQ090024v1_alt, chr13_KQ090025v1_alt, chr13_ML143363v1_fix, chr13_ML143364v1_fix, chr13_ML143365v1_fix, chr13_ML143366v1_fix, chr14_GL000009v2_random, chr14_GL000194v1_random, chr14_KI270722v1_random, chr14_KI270723v1_random, chr14_KI270724v1_random, chr14_KI270725v1_random, chr14_KI270726v1_random, chr14_KI270844v1_alt, chr14_KI270845v1_alt, chr14_KI270846v1_alt, chr14_KI270847v1_alt, chr14_KZ208919v1_alt, chr14_KZ208920v1_fix, chr14_ML143367v1_fix, chr14_ML143368v1_alt, chr15_GL383554v1_alt, chr15_GL383555v2_alt, chr15_KI270727v1_random, chr15_KI270848v1_alt, chr15_KI270849v1_alt, chr15_KI270851v1_alt, chr15_KI270852v1_alt, chr15_KI270906v1_alt, chr15_KN538374v1_fix, chr15_KQ031389v1_alt, chr15_ML143369v1_fix, chr15_ML143370v1_fix, chr15_ML143371v1_fix, chr15_ML143372v1_fix, chr16_GL383556v1_alt, chr16_GL383557v1_alt, chr16_KI270728v1_random, chr16_KI270854v1_alt, chr16_KI270855v1_alt, chr16_KI270856v1_alt, chr16_KQ031390v1_alt, chr16_KQ090026v1_alt, chr16_KQ090027v1_alt, chr16_KV880768v1_fix, chr16_KZ208921v1_alt, chr16_KZ559113v1_fix, chr16_ML143373v1_fix, chr17_GL000258v2_alt, chr17_GL383563v3_alt, chr17_GL383564v2_alt, chr17_GL383565v1_alt, chr17_GL383566v1_alt, chr17_JH159146v1_alt, chr17_JH159147v1_alt, chr17_JH159148v1_alt, chr17_KI270730v1_random, chr17_KI270857v1_alt, chr17_KI270858v1_alt, chr17_KI270859v1_alt, chr17_KI270860v1_alt, chr17_KI270861v1_alt, chr17_KI270862v1_alt, chr17_KI270907v1_alt, chr17_KI270908v1_alt, chr17_KI270909v1_alt, chr17_KI270910v1_alt, chr17_KV575245v1_fix, chr17_KV766196v1_fix, chr17_KV766197v1_alt, chr17_KV766198v1_alt, chr17_KZ559114v1_alt, chr17_ML143374v1_fix, chr17_ML143375v1_fix, chr18_GL383567v1_alt, chr18_GL383568v1_alt, chr18_GL383569v1_alt, chr18_GL383570v1_alt, chr18_GL383571v1_alt, chr18_GL383572v1_alt, chr18_KI270863v1_alt, chr18_KI270864v1_alt, chr18_KI270911v1_alt, chr18_KI270912v1

## >> calculating distance from peak to TSS...   2022-04-20 11:23:00 
## >> assigning genomic annotation...        2022-04-20 11:23:00

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': JTFH01000247.1, JTFH01000515.1, JTFH01000804.1, JTFH01000876.1, JTFH01001024.1, JTFH01001390.1, JTFH01001405.1, JTFH01001430.1, JTFH01001465.1, JTFH01001478.1, JTFH01001512.1, JTFH01001549.1, JTFH01001680.1, JTFH01001724.1, JTFH01001862.1, JTFH01001929.1, JTFH01001959.1, JTFH01001981.1, JTFH01001998.1, KN707720.1, KN707809.1, KN707828.1, KN707893.1, KN707896.1, JTFH01000028.1, JTFH01000280.1, JTFH01000942.1, JTFH01001023.1, JTFH01001317.1, JTFH01001613.1, JTFH01001899.1, KN707626.1
##   - in 'y': chrM, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270706v1_random, chr1_KI270707v1_random, chr1_KI270708v1_random, chr1_KI270709v1_random, chr1_KI270710v1_random, chr1_KI270711v1_random, chr1_KI270712v1_random, chr1_KI270714v1_random, chr1_KI270759v1_alt, chr1_KI270760v1_alt, chr1_KI270761v1_alt, chr1_KI270762v1_alt, chr1_KI270763v1_alt, chr1_KI270764v1_alt, chr1_KI270765v1_alt, chr1_KI270766v1_alt, chr1_KI270892v1_alt, chr1_KN196472v1_fix, chr1_KN196473v1_fix, chr1_KN196474v1_fix, chr1_KN538360v1_fix, chr1_KN538361v1_fix, chr1_KQ031383v1_fix, chr1_KQ458382v1_alt, chr1_KQ458383v1_alt, chr1_KQ458384v1_alt, chr1_KQ983255v1_alt, chr1_KV880763v1_alt, chr1_KZ208904v1_alt, chr1_KZ208905v1_alt, chr1_KZ208906v1_fix, chr1_KZ559100v1_fix, chr2_GL383521v1_alt, chr2_GL383522v1_alt, chr2_GL582966v2_alt, chr2_KI270715v1_random, chr2_KI270716v1_random, chr2_KI270767v1_alt, chr2_KI270768v1_alt, chr2_KI270769v1_alt, chr2_KI270770v1_alt, chr2_KI270771v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270775v1_alt, chr2_KI270776v1_alt, chr2_KI270893v1_alt, chr2_KI270894v1_alt, chr2_KN538362v1_fix, chr2_KN538363v1_fix, chr2_KQ031384v1_fix, chr2_KQ983256v1_alt, chr2_KZ208907v1_alt, chr2_KZ208908v1_alt, chr2_ML143341v1_fix, chr2_ML143342v1_fix, chr3_GL000221v1_random, chr3_GL383526v1_alt, chr3_JH636055v2_alt, chr3_KI270777v1_alt, chr3_KI270778v1_alt, chr3_KI270779v1_alt, chr3_KI270780v1_alt, chr3_KI270781v1_alt, chr3_KI270782v1_alt, chr3_KI270783v1_alt, chr3_KI270784v1_alt, chr3_KI270895v1_alt, chr3_KI270924v1_alt, chr3_KI270934v1_alt, chr3_KI270935v1_alt, chr3_KI270936v1_alt, chr3_KI270937v1_alt, chr3_KN196475v1_fix, chr3_KN196476v1_fix, chr3_KN538364v1_fix, chr3_KQ031385v1_fix, chr3_KQ031386v1_fix, chr3_KV766192v1_fix, chr3_KZ208909v1_alt, chr3_KZ559101v1_alt, chr3_KZ559102v1_alt, chr3_KZ559103v1_alt, chr3_KZ559104v1_fix, chr3_KZ559105v1_alt, chr3_ML143343v1_alt, chr4_GL000008v2_random, chr4_GL000257v2_alt, chr4_GL383528v1_alt, chr4_KI270785v1_alt, chr4_KI270786v1_alt, chr4_KI270787v1_alt, chr4_KI270788v1_alt, chr4_KI270789v1_alt, chr4_KI270790v1_alt, chr4_KI270896v1_alt, chr4_KI270925v1_alt, chr4_KQ090013v1_alt, chr4_KQ090014v1_alt, chr4_KQ090015v1_alt, chr4_KQ983257v1_fix, chr4_KQ983258v1_alt, chr4_KV766193v1_alt, chr4_ML143344v1_fix, chr4_ML143345v1_fix, chr4_ML143346v1_fix, chr4_ML143347v1_fix, chr4_ML143348v1_fix, chr4_ML143349v1_fix, chr5_GL000208v1_random, chr5_GL383530v1_alt, chr5_GL383531v1_alt, chr5_GL383532v1_alt, chr5_GL949742v1_alt, chr5_KI270791v1_alt, chr5_KI270792v1_alt, chr5_KI270793v1_alt, chr5_KI270794v1_alt, chr5_KI270795v1_alt, chr5_KI270796v1_alt, chr5_KI270897v1_alt, chr5_KI270898v1_alt, chr5_KN196477v1_alt, chr5_KV575243v1_alt, chr5_KV575244v1_fix, chr5_KZ208910v1_alt, chr5_ML143350v1_fix, chr6_GL000250v2_alt, chr6_GL000252v2_alt, chr6_GL000253v2_alt, chr6_GL000254v2_alt, chr6_GL000255v2_alt, chr6_GL000256v2_alt, chr6_GL383533v1_alt, chr6_KB021644v2_alt, chr6_KI270758v1_alt, chr6_KI270797v1_alt, chr6_KI270799v1_alt, chr6_KI270800v1_alt, chr6_KI270801v1_alt, chr6_KI270802v1_alt, chr6_KN196478v1_fix, chr6_KQ031387v1_fix, chr6_KQ090016v1_fix, chr6_KQ090017v1_alt, chr6_KV766194v1_fix, chr6_KZ208911v1_fix, chr6_ML143351v1_fix, chr7_GL383534v2_alt, chr7_KI270805v1_alt, chr7_KI270806v1_alt, chr7_KI270807v1_alt, chr7_KI270808v1_alt, chr7_KI270809v1_alt, chr7_KI270899v1_alt, chr7_KQ031388v1_fix, chr7_KV880764v1_fix, chr7_KV880765v1_fix, chr7_KZ208912v1_fix, chr7_KZ208913v1_alt, chr7_KZ559106v1_alt, chr7_ML143352v1_fix, chr8_KI270810v1_alt, chr8_KI270811v1_alt, chr8_KI270812v1_alt, chr8_KI270814v1_alt, chr8_KI270815v1_alt, chr8_KI270816v1_alt, chr8_KI270817v1_alt, chr8_KI270818v1_alt, chr8_KI270819v1_alt, chr8_KI270820v1_alt, chr8_KI270822v1_alt, chr8_KI270900v1_alt, chr8_KI270901v1_alt, chr8_KI270926v1_alt, chr8_KV880766v1_fix, chr8_KV880767v1_fix, chr8_KZ208914v1_fix, chr8_KZ208915v1_fix, chr8_KZ559107v1_alt, chr9_GL383540v1_alt, chr9_GL383541v1_alt, chr9_GL383542v1_alt, chr9_KI270717v1_random, chr9_KI270718v1_random, chr9_KI270719v1_random, chr9_KI270720v1_random, chr9_KI270823v1_alt, chr9_KN196479v1_fix, chr9_KQ090018v1_alt, chr9_KQ090019v1_alt, chr9_ML143353v1_fix, chr10_GL383545v1_alt, chr10_GL383546v1_alt, chr10_KI270824v1_alt, chr10_KI270825v1_alt, chr10_KN196480v1_fix, chr10_KN538365v1_fix, chr10_KN538366v1_fix, chr10_KN538367v1_fix, chr10_KQ090020v1_alt, chr10_KQ090021v1_fix, chr10_ML143354v1_fix, chr10_ML143355v1_fix, chr11_GL383547v1_alt, chr11_JH159136v1_alt, chr11_JH159137v1_alt, chr11_KI270721v1_random, chr11_KI270826v1_alt, chr11_KI270827v1_alt, chr11_KI270829v1_alt, chr11_KI270831v1_alt, chr11_KI270832v1_alt, chr11_KI270902v1_alt, chr11_KI270903v1_alt, chr11_KI270927v1_alt, chr11_KN196481v1_fix, chr11_KN538368v1_alt, chr11_KQ090022v1_fix, chr11_KQ759759v1_fix, chr11_KV766195v1_fix, chr11_KZ559108v1_fix, chr11_KZ559109v1_fix, chr11_KZ559110v1_alt, chr11_KZ559111v1_alt, chr11_ML143356v1_fix, chr11_ML143357v1_fix, chr11_ML143358v1_fix, chr11_ML143359v1_fix, chr11_ML143360v1_fix, chr12_GL383549v1_alt, chr12_GL383550v2_alt, chr12_GL383551v1_alt, chr12_GL383552v1_alt, chr12_GL877875v1_alt, chr12_GL877876v1_alt, chr12_KI270833v1_alt, chr12_KI270834v1_alt, chr12_KI270835v1_alt, chr12_KI270836v1_alt, chr12_KI270837v1_alt, chr12_KI270904v1_alt, chr12_KN196482v1_fix, chr12_KN538369v1_fix, chr12_KN538370v1_fix, chr12_KQ090023v1_alt, chr12_KQ759760v1_fix, chr12_KZ208916v1_fix, chr12_KZ208917v1_fix, chr12_KZ208918v1_alt, chr12_KZ559112v1_alt, chr12_ML143361v1_fix, chr12_ML143362v1_fix, chr13_KI270838v1_alt, chr13_KI270839v1_alt, chr13_KI270840v1_alt, chr13_KI270841v1_alt, chr13_KI270842v1_alt, chr13_KI270843v1_alt, chr13_KN196483v1_fix, chr13_KN538371v1_fix, chr13_KN538372v1_fix, chr13_KN538373v1_fix, chr13_KQ090024v1_alt, chr13_KQ090025v1_alt, chr13_ML143363v1_fix, chr13_ML143364v1_fix, chr13_ML143365v1_fix, chr13_ML143366v1_fix, chr14_GL000009v2_random, chr14_GL000194v1_random, chr14_KI270722v1_random, chr14_KI270723v1_random, chr14_KI270724v1_random, chr14_KI270725v1_random, chr14_KI270726v1_random, chr14_KI270844v1_alt, chr14_KI270845v1_alt, chr14_KI270846v1_alt, chr14_KI270847v1_alt, chr14_KZ208919v1_alt, chr14_KZ208920v1_fix, chr14_ML143367v1_fix, chr14_ML143368v1_alt, chr15_GL383554v1_alt, chr15_GL383555v2_alt, chr15_KI270727v1_random, chr15_KI270848v1_alt, chr15_KI270849v1_alt, chr15_KI270851v1_alt, chr15_KI270852v1_alt, chr15_KI270906v1_alt, chr15_KN538374v1_fix, chr15_KQ031389v1_alt, chr15_ML143369v1_fix, chr15_ML143370v1_fix, chr15_ML143371v1_fix, chr15_ML143372v1_fix, chr16_GL383556v1_alt, chr16_GL383557v1_alt, chr16_KI270728v1_random, chr16_KI270854v1_alt, chr16_KI270855v1_alt, chr16_KI270856v1_alt, chr16_KQ031390v1_alt, chr16_KQ090026v1_alt, chr16_KQ090027v1_alt, chr16_KV880768v1_fix, chr16_KZ208921v1_alt, chr16_KZ559113v1_fix, chr16_ML143373v1_fix, chr17_GL000258v2_alt, chr17_GL383563v3_alt, chr17_GL383564v2_alt, chr17_GL383565v1_alt, chr17_GL383566v1_alt, chr17_JH159146v1_alt, chr17_JH159147v1_alt, chr17_JH159148v1_alt, chr17_KI270730v1_random, chr17_KI270857v1_alt, chr17_KI270858v1_alt, chr17_KI270859v1_alt, chr17_KI270860v1_alt, chr17_KI270861v1_alt, chr17_KI270862v1_alt, chr17_KI270907v1_alt, chr17_KI270908v1_alt, chr17_KI270909v1_alt, chr17_KI270910v1_alt, chr17_KV575245v1_fix, chr17_KV766196v1_fix, chr17_KV766197v1_alt, chr17_KV766198v1_alt, chr17_KZ559114v1_alt, chr17_ML143374v1_fix, chr17_ML143375v1_fix, chr18_GL383567v1_alt, chr18_GL383568v1_alt, chr18_GL383569v1_alt, chr18_GL383570v1_alt, chr18_GL383571v1_alt, chr18_GL383572v1_alt, chr18_KI270863v1_alt, chr18_KI270864v1_alt, chr18_KI270911v1_alt, chr18_KI270912v1

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': JTFH01000247.1, JTFH01000515.1, JTFH01000804.1, JTFH01000876.1, JTFH01001024.1, JTFH01001390.1, JTFH01001405.1, JTFH01001430.1, JTFH01001465.1, JTFH01001478.1, JTFH01001512.1, JTFH01001549.1, JTFH01001680.1, JTFH01001724.1, JTFH01001862.1, JTFH01001929.1, JTFH01001959.1, JTFH01001981.1, JTFH01001998.1, KN707720.1, KN707809.1, KN707828.1, KN707893.1, KN707896.1, JTFH01000028.1, JTFH01000280.1, JTFH01000942.1, JTFH01001023.1, JTFH01001317.1, JTFH01001613.1, JTFH01001899.1, KN707626.1
##   - in 'y': chrM, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270706v1_random, chr1_KI270707v1_random, chr1_KI270708v1_random, chr1_KI270709v1_random, chr1_KI270710v1_random, chr1_KI270711v1_random, chr1_KI270712v1_random, chr1_KI270714v1_random, chr1_KI270759v1_alt, chr1_KI270760v1_alt, chr1_KI270761v1_alt, chr1_KI270762v1_alt, chr1_KI270763v1_alt, chr1_KI270764v1_alt, chr1_KI270765v1_alt, chr1_KI270766v1_alt, chr1_KI270892v1_alt, chr1_KN196472v1_fix, chr1_KN196473v1_fix, chr1_KN196474v1_fix, chr1_KN538360v1_fix, chr1_KN538361v1_fix, chr1_KQ031383v1_fix, chr1_KQ458382v1_alt, chr1_KQ458383v1_alt, chr1_KQ458384v1_alt, chr1_KQ983255v1_alt, chr1_KV880763v1_alt, chr1_KZ208904v1_alt, chr1_KZ208905v1_alt, chr1_KZ208906v1_fix, chr1_KZ559100v1_fix, chr2_GL383521v1_alt, chr2_GL383522v1_alt, chr2_GL582966v2_alt, chr2_KI270715v1_random, chr2_KI270716v1_random, chr2_KI270767v1_alt, chr2_KI270768v1_alt, chr2_KI270769v1_alt, chr2_KI270770v1_alt, chr2_KI270771v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270775v1_alt, chr2_KI270776v1_alt, chr2_KI270893v1_alt, chr2_KI270894v1_alt, chr2_KN538362v1_fix, chr2_KN538363v1_fix, chr2_KQ031384v1_fix, chr2_KQ983256v1_alt, chr2_KZ208907v1_alt, chr2_KZ208908v1_alt, chr2_ML143341v1_fix, chr2_ML143342v1_fix, chr3_GL000221v1_random, chr3_GL383526v1_alt, chr3_JH636055v2_alt, chr3_KI270777v1_alt, chr3_KI270778v1_alt, chr3_KI270779v1_alt, chr3_KI270780v1_alt, chr3_KI270781v1_alt, chr3_KI270782v1_alt, chr3_KI270783v1_alt, chr3_KI270784v1_alt, chr3_KI270895v1_alt, chr3_KI270924v1_alt, chr3_KI270934v1_alt, chr3_KI270935v1_alt, chr3_KI270936v1_alt, chr3_KI270937v1_alt, chr3_KN196475v1_fix, chr3_KN196476v1_fix, chr3_KN538364v1_fix, chr3_KQ031385v1_fix, chr3_KQ031386v1_fix, chr3_KV766192v1_fix, chr3_KZ208909v1_alt, chr3_KZ559101v1_alt, chr3_KZ559102v1_alt, chr3_KZ559103v1_alt, chr3_KZ559104v1_fix, chr3_KZ559105v1_alt, chr3_ML143343v1_alt, chr4_GL000008v2_random, chr4_GL000257v2_alt, chr4_GL383528v1_alt, chr4_KI270785v1_alt, chr4_KI270786v1_alt, chr4_KI270787v1_alt, chr4_KI270788v1_alt, chr4_KI270789v1_alt, chr4_KI270790v1_alt, chr4_KI270896v1_alt, chr4_KI270925v1_alt, chr4_KQ090013v1_alt, chr4_KQ090014v1_alt, chr4_KQ090015v1_alt, chr4_KQ983257v1_fix, chr4_KQ983258v1_alt, chr4_KV766193v1_alt, chr4_ML143344v1_fix, chr4_ML143345v1_fix, chr4_ML143346v1_fix, chr4_ML143347v1_fix, chr4_ML143348v1_fix, chr4_ML143349v1_fix, chr5_GL000208v1_random, chr5_GL383530v1_alt, chr5_GL383531v1_alt, chr5_GL383532v1_alt, chr5_GL949742v1_alt, chr5_KI270791v1_alt, chr5_KI270792v1_alt, chr5_KI270793v1_alt, chr5_KI270794v1_alt, chr5_KI270795v1_alt, chr5_KI270796v1_alt, chr5_KI270897v1_alt, chr5_KI270898v1_alt, chr5_KN196477v1_alt, chr5_KV575243v1_alt, chr5_KV575244v1_fix, chr5_KZ208910v1_alt, chr5_ML143350v1_fix, chr6_GL000250v2_alt, chr6_GL000252v2_alt, chr6_GL000253v2_alt, chr6_GL000254v2_alt, chr6_GL000255v2_alt, chr6_GL000256v2_alt, chr6_GL383533v1_alt, chr6_KB021644v2_alt, chr6_KI270758v1_alt, chr6_KI270797v1_alt, chr6_KI270799v1_alt, chr6_KI270800v1_alt, chr6_KI270801v1_alt, chr6_KI270802v1_alt, chr6_KN196478v1_fix, chr6_KQ031387v1_fix, chr6_KQ090016v1_fix, chr6_KQ090017v1_alt, chr6_KV766194v1_fix, chr6_KZ208911v1_fix, chr6_ML143351v1_fix, chr7_GL383534v2_alt, chr7_KI270805v1_alt, chr7_KI270806v1_alt, chr7_KI270807v1_alt, chr7_KI270808v1_alt, chr7_KI270809v1_alt, chr7_KI270899v1_alt, chr7_KQ031388v1_fix, chr7_KV880764v1_fix, chr7_KV880765v1_fix, chr7_KZ208912v1_fix, chr7_KZ208913v1_alt, chr7_KZ559106v1_alt, chr7_ML143352v1_fix, chr8_KI270810v1_alt, chr8_KI270811v1_alt, chr8_KI270812v1_alt, chr8_KI270814v1_alt, chr8_KI270815v1_alt, chr8_KI270816v1_alt, chr8_KI270817v1_alt, chr8_KI270818v1_alt, chr8_KI270819v1_alt, chr8_KI270820v1_alt, chr8_KI270822v1_alt, chr8_KI270900v1_alt, chr8_KI270901v1_alt, chr8_KI270926v1_alt, chr8_KV880766v1_fix, chr8_KV880767v1_fix, chr8_KZ208914v1_fix, chr8_KZ208915v1_fix, chr8_KZ559107v1_alt, chr9_GL383540v1_alt, chr9_GL383541v1_alt, chr9_GL383542v1_alt, chr9_KI270717v1_random, chr9_KI270718v1_random, chr9_KI270719v1_random, chr9_KI270720v1_random, chr9_KI270823v1_alt, chr9_KN196479v1_fix, chr9_KQ090018v1_alt, chr9_KQ090019v1_alt, chr9_ML143353v1_fix, chr10_GL383545v1_alt, chr10_GL383546v1_alt, chr10_KI270824v1_alt, chr10_KI270825v1_alt, chr10_KN196480v1_fix, chr10_KN538365v1_fix, chr10_KN538366v1_fix, chr10_KN538367v1_fix, chr10_KQ090020v1_alt, chr10_KQ090021v1_fix, chr10_ML143354v1_fix, chr10_ML143355v1_fix, chr11_GL383547v1_alt, chr11_JH159136v1_alt, chr11_JH159137v1_alt, chr11_KI270721v1_random, chr11_KI270826v1_alt, chr11_KI270827v1_alt, chr11_KI270829v1_alt, chr11_KI270831v1_alt, chr11_KI270832v1_alt, chr11_KI270902v1_alt, chr11_KI270903v1_alt, chr11_KI270927v1_alt, chr11_KN196481v1_fix, chr11_KN538368v1_alt, chr11_KQ090022v1_fix, chr11_KQ759759v1_fix, chr11_KV766195v1_fix, chr11_KZ559108v1_fix, chr11_KZ559109v1_fix, chr11_KZ559110v1_alt, chr11_KZ559111v1_alt, chr11_ML143356v1_fix, chr11_ML143357v1_fix, chr11_ML143358v1_fix, chr11_ML143359v1_fix, chr11_ML143360v1_fix, chr12_GL383549v1_alt, chr12_GL383550v2_alt, chr12_GL383551v1_alt, chr12_GL383552v1_alt, chr12_GL877875v1_alt, chr12_GL877876v1_alt, chr12_KI270833v1_alt, chr12_KI270834v1_alt, chr12_KI270835v1_alt, chr12_KI270836v1_alt, chr12_KI270837v1_alt, chr12_KI270904v1_alt, chr12_KN196482v1_fix, chr12_KN538369v1_fix, chr12_KN538370v1_fix, chr12_KQ090023v1_alt, chr12_KQ759760v1_fix, chr12_KZ208916v1_fix, chr12_KZ208917v1_fix, chr12_KZ208918v1_alt, chr12_KZ559112v1_alt, chr12_ML143361v1_fix, chr12_ML143362v1_fix, chr13_KI270838v1_alt, chr13_KI270839v1_alt, chr13_KI270840v1_alt, chr13_KI270841v1_alt, chr13_KI270842v1_alt, chr13_KI270843v1_alt, chr13_KN196483v1_fix, chr13_KN538371v1_fix, chr13_KN538372v1_fix, chr13_KN538373v1_fix, chr13_KQ090024v1_alt, chr13_KQ090025v1_alt, chr13_ML143363v1_fix, chr13_ML143364v1_fix, chr13_ML143365v1_fix, chr13_ML143366v1_fix, chr14_GL000009v2_random, chr14_GL000194v1_random, chr14_KI270722v1_random, chr14_KI270723v1_random, chr14_KI270724v1_random, chr14_KI270725v1_random, chr14_KI270726v1_random, chr14_KI270844v1_alt, chr14_KI270845v1_alt, chr14_KI270846v1_alt, chr14_KI270847v1_alt, chr14_KZ208919v1_alt, chr14_KZ208920v1_fix, chr14_ML143367v1_fix, chr14_ML143368v1_alt, chr15_GL383554v1_alt, chr15_GL383555v2_alt, chr15_KI270727v1_random, chr15_KI270848v1_alt, chr15_KI270849v1_alt, chr15_KI270851v1_alt, chr15_KI270852v1_alt, chr15_KI270906v1_alt, chr15_KN538374v1_fix, chr15_KQ031389v1_alt, chr15_ML143369v1_fix, chr15_ML143370v1_fix, chr15_ML143371v1_fix, chr15_ML143372v1_fix, chr16_GL383556v1_alt, chr16_GL383557v1_alt, chr16_KI270728v1_random, chr16_KI270854v1_alt, chr16_KI270855v1_alt, chr16_KI270856v1_alt, chr16_KQ031390v1_alt, chr16_KQ090026v1_alt, chr16_KQ090027v1_alt, chr16_KV880768v1_fix, chr16_KZ208921v1_alt, chr16_KZ559113v1_fix, chr16_ML143373v1_fix, chr17_GL000258v2_alt, chr17_GL383563v3_alt, chr17_GL383564v2_alt, chr17_GL383565v1_alt, chr17_GL383566v1_alt, chr17_JH159146v1_alt, chr17_JH159147v1_alt, chr17_JH159148v1_alt, chr17_KI270730v1_random, chr17_KI270857v1_alt, chr17_KI270858v1_alt, chr17_KI270859v1_alt, chr17_KI270860v1_alt, chr17_KI270861v1_alt, chr17_KI270862v1_alt, chr17_KI270907v1_alt, chr17_KI270908v1_alt, chr17_KI270909v1_alt, chr17_KI270910v1_alt, chr17_KV575245v1_fix, chr17_KV766196v1_fix, chr17_KV766197v1_alt, chr17_KV766198v1_alt, chr17_KZ559114v1_alt, chr17_ML143374v1_fix, chr17_ML143375v1_fix, chr18_GL383567v1_alt, chr18_GL383568v1_alt, chr18_GL383569v1_alt, chr18_GL383570v1_alt, chr18_GL383571v1_alt, chr18_GL383572v1_alt, chr18_KI270863v1_alt, chr18_KI270864v1_alt, chr18_KI270911v1_alt, chr18_KI270912v1

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': JTFH01000247.1, JTFH01000515.1, JTFH01000804.1, JTFH01000876.1, JTFH01001024.1, JTFH01001390.1, JTFH01001405.1, JTFH01001430.1, JTFH01001465.1, JTFH01001478.1, JTFH01001512.1, JTFH01001549.1, JTFH01001680.1, JTFH01001724.1, JTFH01001862.1, JTFH01001929.1, JTFH01001959.1, JTFH01001981.1, JTFH01001998.1, KN707720.1, KN707809.1, KN707828.1, KN707893.1, KN707896.1, JTFH01000028.1, JTFH01000280.1, JTFH01000942.1, JTFH01001023.1, JTFH01001317.1, JTFH01001613.1, JTFH01001899.1, KN707626.1
##   - in 'y': chrM, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270706v1_random, chr1_KI270707v1_random, chr1_KI270708v1_random, chr1_KI270709v1_random, chr1_KI270710v1_random, chr1_KI270711v1_random, chr1_KI270712v1_random, chr1_KI270714v1_random, chr1_KI270759v1_alt, chr1_KI270760v1_alt, chr1_KI270761v1_alt, chr1_KI270762v1_alt, chr1_KI270763v1_alt, chr1_KI270764v1_alt, chr1_KI270765v1_alt, chr1_KI270766v1_alt, chr1_KI270892v1_alt, chr1_KN196472v1_fix, chr1_KN196473v1_fix, chr1_KN196474v1_fix, chr1_KN538360v1_fix, chr1_KN538361v1_fix, chr1_KQ031383v1_fix, chr1_KQ458382v1_alt, chr1_KQ458383v1_alt, chr1_KQ458384v1_alt, chr1_KQ983255v1_alt, chr1_KV880763v1_alt, chr1_KZ208904v1_alt, chr1_KZ208905v1_alt, chr1_KZ208906v1_fix, chr1_KZ559100v1_fix, chr2_GL383521v1_alt, chr2_GL383522v1_alt, chr2_GL582966v2_alt, chr2_KI270715v1_random, chr2_KI270716v1_random, chr2_KI270767v1_alt, chr2_KI270768v1_alt, chr2_KI270769v1_alt, chr2_KI270770v1_alt, chr2_KI270771v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270775v1_alt, chr2_KI270776v1_alt, chr2_KI270893v1_alt, chr2_KI270894v1_alt, chr2_KN538362v1_fix, chr2_KN538363v1_fix, chr2_KQ031384v1_fix, chr2_KQ983256v1_alt, chr2_KZ208907v1_alt, chr2_KZ208908v1_alt, chr2_ML143341v1_fix, chr2_ML143342v1_fix, chr3_GL000221v1_random, chr3_GL383526v1_alt, chr3_JH636055v2_alt, chr3_KI270777v1_alt, chr3_KI270778v1_alt, chr3_KI270779v1_alt, chr3_KI270780v1_alt, chr3_KI270781v1_alt, chr3_KI270782v1_alt, chr3_KI270783v1_alt, chr3_KI270784v1_alt, chr3_KI270895v1_alt, chr3_KI270924v1_alt, chr3_KI270934v1_alt, chr3_KI270935v1_alt, chr3_KI270936v1_alt, chr3_KI270937v1_alt, chr3_KN196475v1_fix, chr3_KN196476v1_fix, chr3_KN538364v1_fix, chr3_KQ031385v1_fix, chr3_KQ031386v1_fix, chr3_KV766192v1_fix, chr3_KZ208909v1_alt, chr3_KZ559101v1_alt, chr3_KZ559102v1_alt, chr3_KZ559103v1_alt, chr3_KZ559104v1_fix, chr3_KZ559105v1_alt, chr3_ML143343v1_alt, chr4_GL000008v2_random, chr4_GL000257v2_alt, chr4_GL383528v1_alt, chr4_KI270785v1_alt, chr4_KI270786v1_alt, chr4_KI270787v1_alt, chr4_KI270788v1_alt, chr4_KI270789v1_alt, chr4_KI270790v1_alt, chr4_KI270896v1_alt, chr4_KI270925v1_alt, chr4_KQ090013v1_alt, chr4_KQ090014v1_alt, chr4_KQ090015v1_alt, chr4_KQ983257v1_fix, chr4_KQ983258v1_alt, chr4_KV766193v1_alt, chr4_ML143344v1_fix, chr4_ML143345v1_fix, chr4_ML143346v1_fix, chr4_ML143347v1_fix, chr4_ML143348v1_fix, chr4_ML143349v1_fix, chr5_GL000208v1_random, chr5_GL383530v1_alt, chr5_GL383531v1_alt, chr5_GL383532v1_alt, chr5_GL949742v1_alt, chr5_KI270791v1_alt, chr5_KI270792v1_alt, chr5_KI270793v1_alt, chr5_KI270794v1_alt, chr5_KI270795v1_alt, chr5_KI270796v1_alt, chr5_KI270897v1_alt, chr5_KI270898v1_alt, chr5_KN196477v1_alt, chr5_KV575243v1_alt, chr5_KV575244v1_fix, chr5_KZ208910v1_alt, chr5_ML143350v1_fix, chr6_GL000250v2_alt, chr6_GL000252v2_alt, chr6_GL000253v2_alt, chr6_GL000254v2_alt, chr6_GL000255v2_alt, chr6_GL000256v2_alt, chr6_GL383533v1_alt, chr6_KB021644v2_alt, chr6_KI270758v1_alt, chr6_KI270797v1_alt, chr6_KI270799v1_alt, chr6_KI270800v1_alt, chr6_KI270801v1_alt, chr6_KI270802v1_alt, chr6_KN196478v1_fix, chr6_KQ031387v1_fix, chr6_KQ090016v1_fix, chr6_KQ090017v1_alt, chr6_KV766194v1_fix, chr6_KZ208911v1_fix, chr6_ML143351v1_fix, chr7_GL383534v2_alt, chr7_KI270805v1_alt, chr7_KI270806v1_alt, chr7_KI270807v1_alt, chr7_KI270808v1_alt, chr7_KI270809v1_alt, chr7_KI270899v1_alt, chr7_KQ031388v1_fix, chr7_KV880764v1_fix, chr7_KV880765v1_fix, chr7_KZ208912v1_fix, chr7_KZ208913v1_alt, chr7_KZ559106v1_alt, chr7_ML143352v1_fix, chr8_KI270810v1_alt, chr8_KI270811v1_alt, chr8_KI270812v1_alt, chr8_KI270814v1_alt, chr8_KI270815v1_alt, chr8_KI270816v1_alt, chr8_KI270817v1_alt, chr8_KI270818v1_alt, chr8_KI270819v1_alt, chr8_KI270820v1_alt, chr8_KI270822v1_alt, chr8_KI270900v1_alt, chr8_KI270901v1_alt, chr8_KI270926v1_alt, chr8_KV880766v1_fix, chr8_KV880767v1_fix, chr8_KZ208914v1_fix, chr8_KZ208915v1_fix, chr8_KZ559107v1_alt, chr9_GL383540v1_alt, chr9_GL383541v1_alt, chr9_GL383542v1_alt, chr9_KI270717v1_random, chr9_KI270718v1_random, chr9_KI270719v1_random, chr9_KI270720v1_random, chr9_KI270823v1_alt, chr9_KN196479v1_fix, chr9_KQ090018v1_alt, chr9_KQ090019v1_alt, chr9_ML143353v1_fix, chr10_GL383545v1_alt, chr10_GL383546v1_alt, chr10_KI270824v1_alt, chr10_KI270825v1_alt, chr10_KN196480v1_fix, chr10_KN538365v1_fix, chr10_KN538366v1_fix, chr10_KN538367v1_fix, chr10_KQ090020v1_alt, chr10_KQ090021v1_fix, chr10_ML143354v1_fix, chr10_ML143355v1_fix, chr11_GL383547v1_alt, chr11_JH159136v1_alt, chr11_JH159137v1_alt, chr11_KI270721v1_random, chr11_KI270826v1_alt, chr11_KI270827v1_alt, chr11_KI270829v1_alt, chr11_KI270831v1_alt, chr11_KI270832v1_alt, chr11_KI270902v1_alt, chr11_KI270903v1_alt, chr11_KI270927v1_alt, chr11_KN196481v1_fix, chr11_KN538368v1_alt, chr11_KQ090022v1_fix, chr11_KQ759759v1_fix, chr11_KV766195v1_fix, chr11_KZ559108v1_fix, chr11_KZ559109v1_fix, chr11_KZ559110v1_alt, chr11_KZ559111v1_alt, chr11_ML143356v1_fix, chr11_ML143357v1_fix, chr11_ML143358v1_fix, chr11_ML143359v1_fix, chr11_ML143360v1_fix, chr12_GL383549v1_alt, chr12_GL383550v2_alt, chr12_GL383551v1_alt, chr12_GL383552v1_alt, chr12_GL877875v1_alt, chr12_GL877876v1_alt, chr12_KI270833v1_alt, chr12_KI270834v1_alt, chr12_KI270835v1_alt, chr12_KI270836v1_alt, chr12_KI270837v1_alt, chr12_KI270904v1_alt, chr12_KN196482v1_fix, chr12_KN538369v1_fix, chr12_KN538370v1_fix, chr12_KQ090023v1_alt, chr12_KQ759760v1_fix, chr12_KZ208916v1_fix, chr12_KZ208917v1_fix, chr12_KZ208918v1_alt, chr12_KZ559112v1_alt, chr12_ML143361v1_fix, chr12_ML143362v1_fix, chr13_KI270838v1_alt, chr13_KI270839v1_alt, chr13_KI270840v1_alt, chr13_KI270841v1_alt, chr13_KI270842v1_alt, chr13_KI270843v1_alt, chr13_KN196483v1_fix, chr13_KN538371v1_fix, chr13_KN538372v1_fix, chr13_KN538373v1_fix, chr13_KQ090024v1_alt, chr13_KQ090025v1_alt, chr13_ML143363v1_fix, chr13_ML143364v1_fix, chr13_ML143365v1_fix, chr13_ML143366v1_fix, chr14_GL000009v2_random, chr14_GL000194v1_random, chr14_KI270722v1_random, chr14_KI270723v1_random, chr14_KI270724v1_random, chr14_KI270725v1_random, chr14_KI270726v1_random, chr14_KI270844v1_alt, chr14_KI270845v1_alt, chr14_KI270846v1_alt, chr14_KI270847v1_alt, chr14_KZ208919v1_alt, chr14_KZ208920v1_fix, chr14_ML143367v1_fix, chr14_ML143368v1_alt, chr15_GL383554v1_alt, chr15_GL383555v2_alt, chr15_KI270727v1_random, chr15_KI270848v1_alt, chr15_KI270849v1_alt, chr15_KI270851v1_alt, chr15_KI270852v1_alt, chr15_KI270906v1_alt, chr15_KN538374v1_fix, chr15_KQ031389v1_alt, chr15_ML143369v1_fix, chr15_ML143370v1_fix, chr15_ML143371v1_fix, chr15_ML143372v1_fix, chr16_GL383556v1_alt, chr16_GL383557v1_alt, chr16_KI270728v1_random, chr16_KI270854v1_alt, chr16_KI270855v1_alt, chr16_KI270856v1_alt, chr16_KQ031390v1_alt, chr16_KQ090026v1_alt, chr16_KQ090027v1_alt, chr16_KV880768v1_fix, chr16_KZ208921v1_alt, chr16_KZ559113v1_fix, chr16_ML143373v1_fix, chr17_GL000258v2_alt, chr17_GL383563v3_alt, chr17_GL383564v2_alt, chr17_GL383565v1_alt, chr17_GL383566v1_alt, chr17_JH159146v1_alt, chr17_JH159147v1_alt, chr17_JH159148v1_alt, chr17_KI270730v1_random, chr17_KI270857v1_alt, chr17_KI270858v1_alt, chr17_KI270859v1_alt, chr17_KI270860v1_alt, chr17_KI270861v1_alt, chr17_KI270862v1_alt, chr17_KI270907v1_alt, chr17_KI270908v1_alt, chr17_KI270909v1_alt, chr17_KI270910v1_alt, chr17_KV575245v1_fix, chr17_KV766196v1_fix, chr17_KV766197v1_alt, chr17_KV766198v1_alt, chr17_KZ559114v1_alt, chr17_ML143374v1_fix, chr17_ML143375v1_fix, chr18_GL383567v1_alt, chr18_GL383568v1_alt, chr18_GL383569v1_alt, chr18_GL383570v1_alt, chr18_GL383571v1_alt, chr18_GL383572v1_alt, chr18_KI270863v1_alt, chr18_KI270864v1_alt, chr18_KI270911v1_alt, chr18_KI270912v1

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': JTFH01000247.1, JTFH01000515.1, JTFH01000804.1, JTFH01000876.1, JTFH01001024.1, JTFH01001390.1, JTFH01001405.1, JTFH01001430.1, JTFH01001465.1, JTFH01001478.1, JTFH01001512.1, JTFH01001549.1, JTFH01001680.1, JTFH01001724.1, JTFH01001862.1, JTFH01001929.1, JTFH01001959.1, JTFH01001981.1, JTFH01001998.1, KN707720.1, KN707809.1, KN707828.1, KN707893.1, KN707896.1, JTFH01000028.1, JTFH01000280.1, JTFH01000942.1, JTFH01001023.1, JTFH01001317.1, JTFH01001613.1, JTFH01001899.1, KN707626.1
##   - in 'y': chrM, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270706v1_random, chr1_KI270707v1_random, chr1_KI270708v1_random, chr1_KI270709v1_random, chr1_KI270710v1_random, chr1_KI270711v1_random, chr1_KI270712v1_random, chr1_KI270714v1_random, chr1_KI270759v1_alt, chr1_KI270760v1_alt, chr1_KI270761v1_alt, chr1_KI270762v1_alt, chr1_KI270763v1_alt, chr1_KI270764v1_alt, chr1_KI270765v1_alt, chr1_KI270766v1_alt, chr1_KI270892v1_alt, chr1_KN196472v1_fix, chr1_KN196473v1_fix, chr1_KN196474v1_fix, chr1_KN538360v1_fix, chr1_KN538361v1_fix, chr1_KQ031383v1_fix, chr1_KQ458382v1_alt, chr1_KQ458383v1_alt, chr1_KQ458384v1_alt, chr1_KQ983255v1_alt, chr1_KV880763v1_alt, chr1_KZ208904v1_alt, chr1_KZ208905v1_alt, chr1_KZ208906v1_fix, chr1_KZ559100v1_fix, chr2_GL383521v1_alt, chr2_GL383522v1_alt, chr2_GL582966v2_alt, chr2_KI270715v1_random, chr2_KI270716v1_random, chr2_KI270767v1_alt, chr2_KI270768v1_alt, chr2_KI270769v1_alt, chr2_KI270770v1_alt, chr2_KI270771v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270775v1_alt, chr2_KI270776v1_alt, chr2_KI270893v1_alt, chr2_KI270894v1_alt, chr2_KN538362v1_fix, chr2_KN538363v1_fix, chr2_KQ031384v1_fix, chr2_KQ983256v1_alt, chr2_KZ208907v1_alt, chr2_KZ208908v1_alt, chr2_ML143341v1_fix, chr2_ML143342v1_fix, chr3_GL000221v1_random, chr3_GL383526v1_alt, chr3_JH636055v2_alt, chr3_KI270777v1_alt, chr3_KI270778v1_alt, chr3_KI270779v1_alt, chr3_KI270780v1_alt, chr3_KI270781v1_alt, chr3_KI270782v1_alt, chr3_KI270783v1_alt, chr3_KI270784v1_alt, chr3_KI270895v1_alt, chr3_KI270924v1_alt, chr3_KI270934v1_alt, chr3_KI270935v1_alt, chr3_KI270936v1_alt, chr3_KI270937v1_alt, chr3_KN196475v1_fix, chr3_KN196476v1_fix, chr3_KN538364v1_fix, chr3_KQ031385v1_fix, chr3_KQ031386v1_fix, chr3_KV766192v1_fix, chr3_KZ208909v1_alt, chr3_KZ559101v1_alt, chr3_KZ559102v1_alt, chr3_KZ559103v1_alt, chr3_KZ559104v1_fix, chr3_KZ559105v1_alt, chr3_ML143343v1_alt, chr4_GL000008v2_random, chr4_GL000257v2_alt, chr4_GL383528v1_alt, chr4_KI270785v1_alt, chr4_KI270786v1_alt, chr4_KI270787v1_alt, chr4_KI270788v1_alt, chr4_KI270789v1_alt, chr4_KI270790v1_alt, chr4_KI270896v1_alt, chr4_KI270925v1_alt, chr4_KQ090013v1_alt, chr4_KQ090014v1_alt, chr4_KQ090015v1_alt, chr4_KQ983257v1_fix, chr4_KQ983258v1_alt, chr4_KV766193v1_alt, chr4_ML143344v1_fix, chr4_ML143345v1_fix, chr4_ML143346v1_fix, chr4_ML143347v1_fix, chr4_ML143348v1_fix, chr4_ML143349v1_fix, chr5_GL000208v1_random, chr5_GL383530v1_alt, chr5_GL383531v1_alt, chr5_GL383532v1_alt, chr5_GL949742v1_alt, chr5_KI270791v1_alt, chr5_KI270792v1_alt, chr5_KI270793v1_alt, chr5_KI270794v1_alt, chr5_KI270795v1_alt, chr5_KI270796v1_alt, chr5_KI270897v1_alt, chr5_KI270898v1_alt, chr5_KN196477v1_alt, chr5_KV575243v1_alt, chr5_KV575244v1_fix, chr5_KZ208910v1_alt, chr5_ML143350v1_fix, chr6_GL000250v2_alt, chr6_GL000252v2_alt, chr6_GL000253v2_alt, chr6_GL000254v2_alt, chr6_GL000255v2_alt, chr6_GL000256v2_alt, chr6_GL383533v1_alt, chr6_KB021644v2_alt, chr6_KI270758v1_alt, chr6_KI270797v1_alt, chr6_KI270799v1_alt, chr6_KI270800v1_alt, chr6_KI270801v1_alt, chr6_KI270802v1_alt, chr6_KN196478v1_fix, chr6_KQ031387v1_fix, chr6_KQ090016v1_fix, chr6_KQ090017v1_alt, chr6_KV766194v1_fix, chr6_KZ208911v1_fix, chr6_ML143351v1_fix, chr7_GL383534v2_alt, chr7_KI270805v1_alt, chr7_KI270806v1_alt, chr7_KI270807v1_alt, chr7_KI270808v1_alt, chr7_KI270809v1_alt, chr7_KI270899v1_alt, chr7_KQ031388v1_fix, chr7_KV880764v1_fix, chr7_KV880765v1_fix, chr7_KZ208912v1_fix, chr7_KZ208913v1_alt, chr7_KZ559106v1_alt, chr7_ML143352v1_fix, chr8_KI270810v1_alt, chr8_KI270811v1_alt, chr8_KI270812v1_alt, chr8_KI270814v1_alt, chr8_KI270815v1_alt, chr8_KI270816v1_alt, chr8_KI270817v1_alt, chr8_KI270818v1_alt, chr8_KI270819v1_alt, chr8_KI270820v1_alt, chr8_KI270822v1_alt, chr8_KI270900v1_alt, chr8_KI270901v1_alt, chr8_KI270926v1_alt, chr8_KV880766v1_fix, chr8_KV880767v1_fix, chr8_KZ208914v1_fix, chr8_KZ208915v1_fix, chr8_KZ559107v1_alt, chr9_GL383540v1_alt, chr9_GL383541v1_alt, chr9_GL383542v1_alt, chr9_KI270717v1_random, chr9_KI270718v1_random, chr9_KI270719v1_random, chr9_KI270720v1_random, chr9_KI270823v1_alt, chr9_KN196479v1_fix, chr9_KQ090018v1_alt, chr9_KQ090019v1_alt, chr9_ML143353v1_fix, chr10_GL383545v1_alt, chr10_GL383546v1_alt, chr10_KI270824v1_alt, chr10_KI270825v1_alt, chr10_KN196480v1_fix, chr10_KN538365v1_fix, chr10_KN538366v1_fix, chr10_KN538367v1_fix, chr10_KQ090020v1_alt, chr10_KQ090021v1_fix, chr10_ML143354v1_fix, chr10_ML143355v1_fix, chr11_GL383547v1_alt, chr11_JH159136v1_alt, chr11_JH159137v1_alt, chr11_KI270721v1_random, chr11_KI270826v1_alt, chr11_KI270827v1_alt, chr11_KI270829v1_alt, chr11_KI270831v1_alt, chr11_KI270832v1_alt, chr11_KI270902v1_alt, chr11_KI270903v1_alt, chr11_KI270927v1_alt, chr11_KN196481v1_fix, chr11_KN538368v1_alt, chr11_KQ090022v1_fix, chr11_KQ759759v1_fix, chr11_KV766195v1_fix, chr11_KZ559108v1_fix, chr11_KZ559109v1_fix, chr11_KZ559110v1_alt, chr11_KZ559111v1_alt, chr11_ML143356v1_fix, chr11_ML143357v1_fix, chr11_ML143358v1_fix, chr11_ML143359v1_fix, chr11_ML143360v1_fix, chr12_GL383549v1_alt, chr12_GL383550v2_alt, chr12_GL383551v1_alt, chr12_GL383552v1_alt, chr12_GL877875v1_alt, chr12_GL877876v1_alt, chr12_KI270833v1_alt, chr12_KI270834v1_alt, chr12_KI270835v1_alt, chr12_KI270836v1_alt, chr12_KI270837v1_alt, chr12_KI270904v1_alt, chr12_KN196482v1_fix, chr12_KN538369v1_fix, chr12_KN538370v1_fix, chr12_KQ090023v1_alt, chr12_KQ759760v1_fix, chr12_KZ208916v1_fix, chr12_KZ208917v1_fix, chr12_KZ208918v1_alt, chr12_KZ559112v1_alt, chr12_ML143361v1_fix, chr12_ML143362v1_fix, chr13_KI270838v1_alt, chr13_KI270839v1_alt, chr13_KI270840v1_alt, chr13_KI270841v1_alt, chr13_KI270842v1_alt, chr13_KI270843v1_alt, chr13_KN196483v1_fix, chr13_KN538371v1_fix, chr13_KN538372v1_fix, chr13_KN538373v1_fix, chr13_KQ090024v1_alt, chr13_KQ090025v1_alt, chr13_ML143363v1_fix, chr13_ML143364v1_fix, chr13_ML143365v1_fix, chr13_ML143366v1_fix, chr14_GL000009v2_random, chr14_GL000194v1_random, chr14_KI270722v1_random, chr14_KI270723v1_random, chr14_KI270724v1_random, chr14_KI270725v1_random, chr14_KI270726v1_random, chr14_KI270844v1_alt, chr14_KI270845v1_alt, chr14_KI270846v1_alt, chr14_KI270847v1_alt, chr14_KZ208919v1_alt, chr14_KZ208920v1_fix, chr14_ML143367v1_fix, chr14_ML143368v1_alt, chr15_GL383554v1_alt, chr15_GL383555v2_alt, chr15_KI270727v1_random, chr15_KI270848v1_alt, chr15_KI270849v1_alt, chr15_KI270851v1_alt, chr15_KI270852v1_alt, chr15_KI270906v1_alt, chr15_KN538374v1_fix, chr15_KQ031389v1_alt, chr15_ML143369v1_fix, chr15_ML143370v1_fix, chr15_ML143371v1_fix, chr15_ML143372v1_fix, chr16_GL383556v1_alt, chr16_GL383557v1_alt, chr16_KI270728v1_random, chr16_KI270854v1_alt, chr16_KI270855v1_alt, chr16_KI270856v1_alt, chr16_KQ031390v1_alt, chr16_KQ090026v1_alt, chr16_KQ090027v1_alt, chr16_KV880768v1_fix, chr16_KZ208921v1_alt, chr16_KZ559113v1_fix, chr16_ML143373v1_fix, chr17_GL000258v2_alt, chr17_GL383563v3_alt, chr17_GL383564v2_alt, chr17_GL383565v1_alt, chr17_GL383566v1_alt, chr17_JH159146v1_alt, chr17_JH159147v1_alt, chr17_JH159148v1_alt, chr17_KI270730v1_random, chr17_KI270857v1_alt, chr17_KI270858v1_alt, chr17_KI270859v1_alt, chr17_KI270860v1_alt, chr17_KI270861v1_alt, chr17_KI270862v1_alt, chr17_KI270907v1_alt, chr17_KI270908v1_alt, chr17_KI270909v1_alt, chr17_KI270910v1_alt, chr17_KV575245v1_fix, chr17_KV766196v1_fix, chr17_KV766197v1_alt, chr17_KV766198v1_alt, chr17_KZ559114v1_alt, chr17_ML143374v1_fix, chr17_ML143375v1_fix, chr18_GL383567v1_alt, chr18_GL383568v1_alt, chr18_GL383569v1_alt, chr18_GL383570v1_alt, chr18_GL383571v1_alt, chr18_GL383572v1_alt, chr18_KI270863v1_alt, chr18_KI270864v1_alt, chr18_KI270911v1_alt, chr18_KI270912v1

## >> adding gene annotation...          2022-04-20 11:23:04

## 'select()' returned 1:many mapping between keys and columns

## >> assigning chromosome lengths           2022-04-20 11:23:04 
## >> done...                    2022-04-20 11:23:04

plotFeatureDist(res.lfcShrink.granges.ChIPseeker@anno$distanceToTSS,
    featureName = "TSS", nbins = 20)

## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.

## Scale for 'x' is already present. Adding another scale for 'x', which will
## replace the existing scale.

plotFeatureDist(res.lfcShrink.granges.ChIPseeker.background@anno$distanceToTSS,
    featureName = "TSS", nbins = 20)

## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.

## Scale for 'x' is already present. Adding another scale for 'x', which will
## replace the existing scale.

Annotate results

blkList <- import.bed("/Volumes/GoogleDrive/My Drive/Greally_Lab/Toxoplasma/Genomes/GRCh38/ENCFF356LFX.bed.gz")
annoDataTxDb <- toGRanges(TxDb.Hsapiens.UCSC.hg38.knownGene)

res.lfcShrink.granges.annot <- res.lfcShrink.granges

# remove blacklisted peaks
res.lfcShrink.granges.annot <- res.lfcShrink.granges.annot[!res.lfcShrink.granges.annot %over%
    blkList]

# keep the seqnames in the same style
if (!identical(seqlevelsStyle(res.lfcShrink.granges.annot), seqlevelsStyle(annoDataTxDb))) {
    seqlevelsStyle(res.lfcShrink.granges.annot) <- seqlevelsStyle(annoDataTxDb)[1]
}

# do annotation by nearest TSS of UCSC hg38 annotations
res.lfcShrink.granges.annot <- annotatePeakInBatch(res.lfcShrink.granges.annot,
    AnnotationData = annoDataTxDb, select = "all", output = "overlapping",
    FeatureLocForDistance = "TSS", PeakLocForDistance = "middle",
    bindingRegion = c(-5000, 5000))

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': JTFH01000247.1, JTFH01000515.1, JTFH01000804.1, JTFH01000876.1, JTFH01001024.1, JTFH01001390.1, JTFH01001405.1, JTFH01001430.1, JTFH01001465.1, JTFH01001478.1, JTFH01001512.1, JTFH01001549.1, JTFH01001680.1, JTFH01001724.1, JTFH01001862.1, JTFH01001929.1, JTFH01001959.1, JTFH01001981.1, JTFH01001998.1, KN707720.1, KN707809.1, KN707828.1, KN707893.1, KN707896.1, JTFH01000028.1, JTFH01000280.1, JTFH01000942.1, JTFH01001023.1, JTFH01001317.1, JTFH01001613.1, JTFH01001899.1, KN707626.1
##   - in 'y': chrM, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270706v1_random, chr1_KI270707v1_random, chr1_KI270708v1_random, chr1_KI270709v1_random, chr1_KI270710v1_random, chr1_KI270711v1_random, chr1_KI270712v1_random, chr1_KI270714v1_random, chr1_KI270759v1_alt, chr1_KI270760v1_alt, chr1_KI270761v1_alt, chr1_KI270762v1_alt, chr1_KI270763v1_alt, chr1_KI270764v1_alt, chr1_KI270765v1_alt, chr1_KI270766v1_alt, chr1_KI270892v1_alt, chr1_KN196472v1_fix, chr1_KN196473v1_fix, chr1_KN196474v1_fix, chr1_KN538360v1_fix, chr1_KN538361v1_fix, chr1_KQ031383v1_fix, chr1_KQ458382v1_alt, chr1_KQ458383v1_alt, chr1_KQ458384v1_alt, chr1_KQ983255v1_alt, chr1_KV880763v1_alt, chr1_KZ208904v1_alt, chr1_KZ208905v1_alt, chr1_KZ208906v1_fix, chr1_KZ559100v1_fix, chr2_GL383521v1_alt, chr2_GL383522v1_alt, chr2_GL582966v2_alt, chr2_KI270715v1_random, chr2_KI270716v1_random, chr2_KI270767v1_alt, chr2_KI270768v1_alt, chr2_KI270769v1_alt, chr2_KI270770v1_alt, chr2_KI270771v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270775v1_alt, chr2_KI270776v1_alt, chr2_KI270893v1_alt, chr2_KI270894v1_alt, chr2_KN538362v1_fix, chr2_KN538363v1_fix, chr2_KQ031384v1_fix, chr2_KQ983256v1_alt, chr2_KZ208907v1_alt, chr2_KZ208908v1_alt, chr2_ML143341v1_fix, chr2_ML143342v1_fix, chr3_GL000221v1_random, chr3_GL383526v1_alt, chr3_JH636055v2_alt, chr3_KI270777v1_alt, chr3_KI270778v1_alt, chr3_KI270779v1_alt, chr3_KI270780v1_alt, chr3_KI270781v1_alt, chr3_KI270782v1_alt, chr3_KI270783v1_alt, chr3_KI270784v1_alt, chr3_KI270895v1_alt, chr3_KI270924v1_alt, chr3_KI270934v1_alt, chr3_KI270935v1_alt, chr3_KI270936v1_alt, chr3_KI270937v1_alt, chr3_KN196475v1_fix, chr3_KN196476v1_fix, chr3_KN538364v1_fix, chr3_KQ031385v1_fix, chr3_KQ031386v1_fix, chr3_KV766192v1_fix, chr3_KZ208909v1_alt, chr3_KZ559101v1_alt, chr3_KZ559102v1_alt, chr3_KZ559103v1_alt, chr3_KZ559104v1_fix, chr3_KZ559105v1_alt, chr3_ML143343v1_alt, chr4_GL000008v2_random, chr4_GL000257v2_alt, chr4_GL383528v1_alt, chr4_KI270785v1_alt, chr4_KI270786v1_alt, chr4_KI270787v1_alt, chr4_KI270788v1_alt, chr4_KI270789v1_alt, chr4_KI270790v1_alt, chr4_KI270896v1_alt, chr4_KI270925v1_alt, chr4_KQ090013v1_alt, chr4_KQ090014v1_alt, chr4_KQ090015v1_alt, chr4_KQ983257v1_fix, chr4_KQ983258v1_alt, chr4_KV766193v1_alt, chr4_ML143344v1_fix, chr4_ML143345v1_fix, chr4_ML143346v1_fix, chr4_ML143347v1_fix, chr4_ML143348v1_fix, chr4_ML143349v1_fix, chr5_GL000208v1_random, chr5_GL383530v1_alt, chr5_GL383531v1_alt, chr5_GL383532v1_alt, chr5_GL949742v1_alt, chr5_KI270791v1_alt, chr5_KI270792v1_alt, chr5_KI270793v1_alt, chr5_KI270794v1_alt, chr5_KI270795v1_alt, chr5_KI270796v1_alt, chr5_KI270897v1_alt, chr5_KI270898v1_alt, chr5_KN196477v1_alt, chr5_KV575243v1_alt, chr5_KV575244v1_fix, chr5_KZ208910v1_alt, chr5_ML143350v1_fix, chr6_GL000250v2_alt, chr6_GL000252v2_alt, chr6_GL000253v2_alt, chr6_GL000254v2_alt, chr6_GL000255v2_alt, chr6_GL000256v2_alt, chr6_GL383533v1_alt, chr6_KB021644v2_alt, chr6_KI270758v1_alt, chr6_KI270797v1_alt, chr6_KI270799v1_alt, chr6_KI270800v1_alt, chr6_KI270801v1_alt, chr6_KI270802v1_alt, chr6_KN196478v1_fix, chr6_KQ031387v1_fix, chr6_KQ090016v1_fix, chr6_KQ090017v1_alt, chr6_KV766194v1_fix, chr6_KZ208911v1_fix, chr6_ML143351v1_fix, chr7_GL383534v2_alt, chr7_KI270805v1_alt, chr7_KI270806v1_alt, chr7_KI270807v1_alt, chr7_KI270808v1_alt, chr7_KI270809v1_alt, chr7_KI270899v1_alt, chr7_KQ031388v1_fix, chr7_KV880764v1_fix, chr7_KV880765v1_fix, chr7_KZ208912v1_fix, chr7_KZ208913v1_alt, chr7_KZ559106v1_alt, chr7_ML143352v1_fix, chr8_KI270810v1_alt, chr8_KI270811v1_alt, chr8_KI270812v1_alt, chr8_KI270814v1_alt, chr8_KI270815v1_alt, chr8_KI270816v1_alt, chr8_KI270817v1_alt, chr8_KI270818v1_alt, chr8_KI270819v1_alt, chr8_KI270820v1_alt, chr8_KI270822v1_alt, chr8_KI270900v1_alt, chr8_KI270901v1_alt, chr8_KI270926v1_alt, chr8_KV880766v1_fix, chr8_KV880767v1_fix, chr8_KZ208914v1_fix, chr8_KZ208915v1_fix, chr8_KZ559107v1_alt, chr9_GL383540v1_alt, chr9_GL383541v1_alt, chr9_GL383542v1_alt, chr9_KI270717v1_random, chr9_KI270718v1_random, chr9_KI270719v1_random, chr9_KI270720v1_random, chr9_KI270823v1_alt, chr9_KN196479v1_fix, chr9_KQ090018v1_alt, chr9_KQ090019v1_alt, chr9_ML143353v1_fix, chr10_GL383545v1_alt, chr10_GL383546v1_alt, chr10_KI270824v1_alt, chr10_KI270825v1_alt, chr10_KN196480v1_fix, chr10_KN538365v1_fix, chr10_KN538366v1_fix, chr10_KN538367v1_fix, chr10_KQ090020v1_alt, chr10_KQ090021v1_fix, chr10_ML143354v1_fix, chr10_ML143355v1_fix, chr11_GL383547v1_alt, chr11_JH159136v1_alt, chr11_JH159137v1_alt, chr11_KI270721v1_random, chr11_KI270826v1_alt, chr11_KI270827v1_alt, chr11_KI270829v1_alt, chr11_KI270831v1_alt, chr11_KI270832v1_alt, chr11_KI270902v1_alt, chr11_KI270903v1_alt, chr11_KI270927v1_alt, chr11_KN196481v1_fix, chr11_KN538368v1_alt, chr11_KQ090022v1_fix, chr11_KQ759759v1_fix, chr11_KV766195v1_fix, chr11_KZ559108v1_fix, chr11_KZ559109v1_fix, chr11_KZ559110v1_alt, chr11_KZ559111v1_alt, chr11_ML143356v1_fix, chr11_ML143357v1_fix, chr11_ML143358v1_fix, chr11_ML143359v1_fix, chr11_ML143360v1_fix, chr12_GL383549v1_alt, chr12_GL383550v2_alt, chr12_GL383551v1_alt, chr12_GL383552v1_alt, chr12_GL877875v1_alt, chr12_GL877876v1_alt, chr12_KI270833v1_alt, chr12_KI270834v1_alt, chr12_KI270835v1_alt, chr12_KI270836v1_alt, chr12_KI270837v1_alt, chr12_KI270904v1_alt, chr12_KN196482v1_fix, chr12_KN538369v1_fix, chr12_KN538370v1_fix, chr12_KQ090023v1_alt, chr12_KQ759760v1_fix, chr12_KZ208916v1_fix, chr12_KZ208917v1_fix, chr12_KZ208918v1_alt, chr12_KZ559112v1_alt, chr12_ML143361v1_fix, chr12_ML143362v1_fix, chr13_KI270838v1_alt, chr13_KI270839v1_alt, chr13_KI270840v1_alt, chr13_KI270841v1_alt, chr13_KI270842v1_alt, chr13_KI270843v1_alt, chr13_KN196483v1_fix, chr13_KN538371v1_fix, chr13_KN538372v1_fix, chr13_KN538373v1_fix, chr13_KQ090024v1_alt, chr13_KQ090025v1_alt, chr13_ML143363v1_fix, chr13_ML143364v1_fix, chr13_ML143365v1_fix, chr13_ML143366v1_fix, chr14_GL000009v2_random, chr14_GL000194v1_random, chr14_KI270722v1_random, chr14_KI270723v1_random, chr14_KI270724v1_random, chr14_KI270725v1_random, chr14_KI270726v1_random, chr14_KI270844v1_alt, chr14_KI270845v1_alt, chr14_KI270846v1_alt, chr14_KI270847v1_alt, chr14_KZ208919v1_alt, chr14_KZ208920v1_fix, chr14_ML143367v1_fix, chr14_ML143368v1_alt, chr15_GL383554v1_alt, chr15_GL383555v2_alt, chr15_KI270727v1_random, chr15_KI270848v1_alt, chr15_KI270849v1_alt, chr15_KI270851v1_alt, chr15_KI270852v1_alt, chr15_KI270906v1_alt, chr15_KN538374v1_fix, chr15_KQ031389v1_alt, chr15_ML143369v1_fix, chr15_ML143370v1_fix, chr15_ML143371v1_fix, chr15_ML143372v1_fix, chr16_GL383556v1_alt, chr16_GL383557v1_alt, chr16_KI270728v1_random, chr16_KI270854v1_alt, chr16_KI270855v1_alt, chr16_KI270856v1_alt, chr16_KQ031390v1_alt, chr16_KQ090026v1_alt, chr16_KQ090027v1_alt, chr16_KV880768v1_fix, chr16_KZ208921v1_alt, chr16_KZ559113v1_fix, chr16_ML143373v1_fix, chr17_GL000258v2_alt, chr17_GL383563v3_alt, chr17_GL383564v2_alt, chr17_GL383565v1_alt, chr17_GL383566v1_alt, chr17_JH159146v1_alt, chr17_JH159147v1_alt, chr17_JH159148v1_alt, chr17_KI270730v1_random, chr17_KI270857v1_alt, chr17_KI270858v1_alt, chr17_KI270859v1_alt, chr17_KI270860v1_alt, chr17_KI270861v1_alt, chr17_KI270862v1_alt, chr17_KI270907v1_alt, chr17_KI270908v1_alt, chr17_KI270909v1_alt, chr17_KI270910v1_alt, chr17_KV575245v1_fix, chr17_KV766196v1_fix, chr17_KV766197v1_alt, chr17_KV766198v1_alt, chr17_KZ559114v1_alt, chr17_ML143374v1_fix, chr17_ML143375v1_fix, chr18_GL383567v1_alt, chr18_GL383568v1_alt, chr18_GL383569v1_alt, chr18_GL383570v1_alt, chr18_GL383571v1_alt, chr18_GL383572v1_alt, chr18_KI270863v1_alt, chr18_KI270864v1_alt, chr18_KI270911v1_alt, chr18_KI270912v1

head(res.lfcShrink.granges.annot, n = 2)

## GRanges object with 2 ranges and 17 metadata columns:
##       seqnames              ranges strand |  baseMean log2FoldChange     lfcSE
##          <Rle>           <IRanges>  <Rle> | <numeric>      <numeric> <numeric>
##    X3     chr1   74673758-74674374      * |   50.2600        3.26583   0.41158
##   X10    chr11 115925001-115925460      * |   27.0066        5.09635   0.82382
##            pvalue        padj        I2        I3        U1        U2        U3
##         <numeric>   <numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
##    X3 9.57734e-17 8.52575e-13  113.3812  105.4563  5.854591   14.2922  12.31558
##   X10 1.52156e-12 4.06347e-09   62.5186   69.8091  0.532236    0.0000   2.17334
##              peak     feature      feature.ranges feature.strand  distance
##       <character> <character>           <IRanges>          <Rle> <integer>
##    X3          X3      127254   74568117-74673792              -         0
##   X10         X10   102724165 115920248-115943181              +         0
##       insideFeature distanceToSite
##         <character>      <integer>
##    X3  overlapStart              0
##   X10        inside           4752
##   -------
##   seqinfo: 88 sequences from an unspecified genome; no seqlengths

# get distance of DARs from TSS
res.lfcShrink.granges.DAR <- annotatePeakInBatch(res.lfcShrink.granges[res.lfcShrink.granges$padj <
    0.05, ], AnnotationData = annoDataTxDb, select = "first",
    output = "nearestLocation", FeatureLocForDistance = "TSS",
    PeakLocForDistance = "middle", bindingRegion = c(-1e+05,
        1e+05))

## Warning in annotatePeakInBatch(res.lfcShrink.granges[res.lfcShrink.granges$padj < : not all the seqnames of myPeakList is 
##                     in the AnnotationData.

## Warning in annotatePeakInBatch(res.lfcShrink.granges[res.lfcShrink.granges$padj < : Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': JTFH01000247.1, JTFH01000515.1, JTFH01000804.1, JTFH01000876.1, JTFH01001024.1, JTFH01001390.1, JTFH01001405.1, JTFH01001430.1, JTFH01001465.1, JTFH01001478.1, JTFH01001512.1, JTFH01001549.1, JTFH01001680.1, JTFH01001724.1, JTFH01001862.1, JTFH01001929.1, JTFH01001959.1, JTFH01001981.1, JTFH01001998.1, KN707720.1, KN707809.1, KN707828.1, KN707893.1, KN707896.1, JTFH01000028.1, JTFH01000280.1, JTFH01000942.1, JTFH01001023.1, JTFH01001317.1, JTFH01001613.1, JTFH01001899.1, KN707626.1
##   - in 'y': chrM, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270706v1_random, chr1_KI270707v1_random, chr1_KI270708v1_random, chr1_KI270709v1_random, chr1_KI270710v1_random, chr1_KI270711v1_random, chr1_KI270712v1_random, chr1_KI270714v1_random, chr1_KI270759v1_alt, chr1_KI270760v1_alt, chr1_KI270761v1_alt, chr1_KI270762v1_alt, chr1_KI270763v1_alt, chr1_KI270764v1_alt, chr1_KI270765v1_alt, chr1_KI270766v1_alt, chr1_KI270892v1_alt, chr1_KN196472v1_fix, chr1_KN196473v1_fix, chr1_KN196474v1_fix, chr1_KN538360v1_fix, chr1_KN538361v1_fix, chr1_KQ031383v1_fix, chr1_KQ458382v1_alt, chr1_KQ458383v1_alt, chr1_KQ458384v1_alt, chr1_KQ983255v1_alt, chr1_KV880763v1_alt, chr1_KZ208904v1_alt, chr1_KZ208905v1_alt, chr1_KZ208906v1_fix, chr1_KZ559100v1_fix, chr2_GL383521v1_alt, chr2_GL383522v1_alt, chr2_GL582966v2_alt, chr2_KI270715v1_random, chr2_KI270716v1_random, chr2_KI270767v1_alt, chr2_KI270768v1_alt, chr2_KI270769v1_alt, chr2_KI270770v1_alt, chr2_KI270771v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270775v1_alt, chr2_KI270776v1_alt, chr2_KI270893v1_alt, chr2_KI270894v1_alt, chr2_KN538362v1_fix, chr2_KN538363v1_fix, chr2_KQ031384v1_fix, chr2_KQ983256v1_alt, chr2_KZ208907v1_alt, chr2_KZ208908v1_alt, chr2_ML143341v1_fix, chr2_ML143342v1_fix, chr3_GL000221v1_random, chr3_GL383526v1_alt, chr3_JH636055v2_alt, chr3_KI270777v1_alt, chr3_KI270778v1_alt, chr3_KI270779v1_alt, chr3_KI270780v1_alt, chr3_KI270781v1_alt, chr3_KI270782v1_alt, chr3_KI270783v1_alt, chr3_KI270784v1_alt, chr3_KI270895v1_alt, chr3_KI270924v1_alt, chr3_KI270934v1_alt, chr3_KI270935v1_alt, chr3_KI270936v1_alt, chr3_KI270937v1_alt, chr3_KN196475v1_fix, chr3_KN196476v1_fix, chr3_KN538364v1_fix, chr3_KQ031385v1_fix, chr3_KQ031386v1_fix, chr3_KV766192v1_fix, chr3_KZ208909v1_alt, chr3_KZ559101v1_alt, chr3_KZ559102v1_alt, chr3_KZ559103v1_alt, chr3_KZ559104v1_fix, chr3_KZ559105v1_alt, chr3_ML143343v1_alt, chr4_GL000008v2_random, chr4_GL000257v2_alt, chr4_GL383528v1_alt, chr4_KI270785v1_alt, chr4_KI270786v1_alt, chr4_KI270787v1_alt, chr4_KI270788v1_alt, chr4_KI270789v1_alt, chr4_KI270790v1_alt, chr4_KI270896v1_alt, chr4_KI270925v1_alt, chr4_KQ090013v1_alt, chr4_KQ090014v1_alt, chr4_KQ090015v1_alt, chr4_KQ983257v1_fix, chr4_KQ983258v1_alt, chr4_KV766193v1_alt, chr4_ML143344v1_fix, chr4_ML143345v1_fix, chr4_ML143346v1_fix, chr4_ML143347v1_fix, chr4_ML143348v1_fix, chr4_ML143349v1_fix, chr5_GL000208v1_random, chr5_GL383530v1_alt, chr5_GL383531v1_alt, chr5_GL383532v1_alt, chr5_GL949742v1_alt, chr5_KI270791v1_alt, chr5_KI270792v1_alt, chr5_KI270793v1_alt, chr5_KI270794v1_alt, chr5_KI270795v1_alt, chr5_KI270796v1_alt, chr5_KI270897v1_alt, chr5_KI270898v1_alt, chr5_KN196477v1_alt, chr5_KV575243v1_alt, chr5_KV575244v1_fix, chr5_KZ208910v1_alt, chr5_ML143350v1_fix, chr6_GL000250v2_alt, chr6_GL000252v2_alt, chr6_GL000253v2_alt, chr6_GL000254v2_alt, chr6_GL000255v2_alt, chr6_GL000256v2_alt, chr6_GL383533v1_alt, chr6_KB021644v2_alt, chr6_KI270758v1_alt, chr6_KI270797v1_alt, chr6_KI270799v1_alt, chr6_KI270800v1_alt, chr6_KI270801v1_alt, chr6_KI270802v1_alt, chr6_KN196478v1_fix, chr6_KQ031387v1_fix, chr6_KQ090016v1_fix, chr6_KQ090017v1_alt, chr6_KV766194v1_fix, chr6_KZ208911v1_fix, chr6_ML143351v1_fix, chr7_GL383534v2_alt, chr7_KI270805v1_alt, chr7_KI270806v1_alt, chr7_KI270807v1_alt, chr7_KI270808v1_alt, chr7_KI270809v1_alt, chr7_KI270899v1_alt, chr7_KQ031388v1_fix, chr7_KV880764v1_fix, chr7_KV880765v1_fix, chr7_KZ208912v1_fix, chr7_KZ208913v1_alt, chr7_KZ559106v1_alt, chr7_ML143352v1_fix, chr8_KI270810v1_alt, chr8_KI270811v1_alt, chr8_KI270812v1_alt, chr8_KI270814v1_alt, chr8_KI270815v1_alt, chr8_KI270816v1_alt, chr8_KI270817v1_alt, chr8_KI270818v1_alt, chr8_KI270819v1_alt, chr8_KI270820v1_alt, chr8_KI270822v1_alt, chr8_KI270900v1_alt, chr8_KI270901v1_alt, chr8_KI270926v1_alt, chr8_KV880766v1_fix, chr8_KV880767v1_fix, chr8_KZ208914v1_fix, chr8_KZ208915v1_fix, chr8_KZ559107v1_alt, chr9_GL383540v1_alt, chr9_GL383541v1_alt, chr9_GL383542v1_alt, chr9_KI270717v1_random, chr9_KI270718v1_random, chr9_KI270719v1_random, chr9_KI270720v1_random, chr9_KI270823v1_alt, chr9_KN196479v1_fix, chr9_KQ090018v1_alt, chr9_KQ090019v1_alt, chr9_ML143353v1_fix, chr10_GL383545v1_alt, chr10_GL383546v1_alt, chr10_KI270824v1_alt, chr10_KI270825v1_alt, chr10_KN196480v1_fix, chr10_KN538365v1_fix, chr10_KN538366v1_fix, chr10_KN538367v1_fix, chr10_KQ090020v1_alt, chr10_KQ090021v1_fix, chr10_ML143354v1_fix, chr10_ML143355v1_fix, chr11_GL383547v1_alt, chr11_JH159136v1_alt, chr11_JH159137v1_alt, chr11_KI270721v1_random, chr11_KI270826v1_alt, chr11_KI270827v1_alt, chr11_KI270829v1_alt, chr11_KI270831v1_alt, chr11_KI270832v1_alt, chr11_KI270902v1_alt, chr11_KI270903v1_alt, chr11_KI270927v1_alt, chr11_KN196481v1_fix, chr11_KN538368v1_alt, chr11_KQ090022v1_fix, chr11_KQ759759v1_fix, chr11_KV766195v1_fix, chr11_KZ559108v1_fix, chr11_KZ559109v1_fix, chr11_KZ559110v1_alt, chr11_KZ559111v1_alt, chr11_ML143356v1_fix, chr11_ML143357v1_fix, chr11_ML143358v1_fix, chr11_ML143359v1_fix, chr11_ML143360v1_fix, chr12_GL383549v1_alt, chr12_GL383550v2_alt, chr12_GL383551v1_alt, chr12_GL383552v1_alt, chr12_GL877875v1_alt, chr12_GL877876v1_alt, chr12_KI270833v1_alt, chr12_KI270834v1_alt, chr12_KI270835v1_alt, chr12_KI270836v1_alt, chr12_KI270837v1_alt, chr12_KI270904v1_alt, chr12_KN196482v1_fix, chr12_KN538369v1_fix, chr12_KN538370v1_fix, chr12_KQ090023v1_alt, chr12_KQ759760v1_fix, chr12_KZ208916v1_fix, chr12_KZ208917v1_fix, chr12_KZ208918v1_alt, chr12_KZ559112v1_alt, chr12_ML143361v1_fix, chr12_ML143362v1_fix, chr13_KI270838v1_alt, chr13_KI270839v1_alt, chr13_KI270840v1_alt, chr13_KI270841v1_alt, chr13_KI270842v1_alt, chr13_KI270843v1_alt, chr13_KN196483v1_fix, chr13_KN538371v1_fix, chr13_KN538372v1_fix, chr13_KN538373v1_fix, chr13_KQ090024v1_alt, chr13_KQ090025v1_alt, chr13_ML143363v1_fix, chr13_ML143364v1_fix, chr13_ML143365v1_fix, chr13_ML143366v1_fix, chr14_GL000009v2_random, chr14_GL000194v1_random, chr14_KI270722v1_random, chr14_KI270723v1_random, chr14_KI270724v1_random, chr14_KI270725v1_random, chr14_KI270726v1_random, chr14_KI270844v1_alt, chr14_KI270845v1_alt, chr14_KI270846v1_alt, chr14_KI270847v1_alt, chr14_KZ208919v1_alt, chr14_KZ208920v1_fix, chr14_ML143367v1_fix, chr14_ML143368v1_alt, chr15_GL383554v1_alt, chr15_GL383555v2_alt, chr15_KI270727v1_random, chr15_KI270848v1_alt, chr15_KI270849v1_alt, chr15_KI270851v1_alt, chr15_KI270852v1_alt, chr15_KI270906v1_alt, chr15_KN538374v1_fix, chr15_KQ031389v1_alt, chr15_ML143369v1_fix, chr15_ML143370v1_fix, chr15_ML143371v1_fix, chr15_ML143372v1_fix, chr16_GL383556v1_alt, chr16_GL383557v1_alt, chr16_KI270728v1_random, chr16_KI270854v1_alt, chr16_KI270855v1_alt, chr16_KI270856v1_alt, chr16_KQ031390v1_alt, chr16_KQ090026v1_alt, chr16_KQ090027v1_alt, chr16_KV880768v1_fix, chr16_KZ208921v1_alt, chr16_KZ559113v1_fix, chr16_ML143373v1_fix, chr17_GL000258v2_alt, chr17_GL383563v3_alt, chr17_GL383564v2_alt, chr17_GL383565v1_alt, chr17_GL383566v1_alt, chr17_JH159146v1_alt, chr17_JH159147v1_alt, chr17_JH159148v1_alt, chr17_KI270730v1_random, chr17_KI270857v1_alt, chr17_KI270858v1_alt, chr17_KI270859v1_alt, chr17_KI270860v1_alt, chr17_KI270861v1_alt, chr17_KI270862v1_alt, chr17_KI270907v1_alt, chr17_KI270908v1_alt, chr17_KI270909v1_alt, chr17_KI270910v1_alt, chr17_KV575245v1_fix, chr17_KV766196v1_fix, chr17_KV766197v1_alt, chr17_KV766198v1_alt, chr17_KZ559114v1_alt, chr17_ML143374v1_fix, chr17_ML143375v1_fix, chr18_GL383567v1_alt, chr18_GL383568v1_alt, chr18_GL383569v1_alt, chr18_GL383570v1_alt, chr18_GL383571v1_alt, chr18_GL383572v1_alt, chr18_KI270863v1_alt, chr18_KI270864v1_alt, chr18_KI270911v1_alt, chr18_KI270912v1

hist(res.lfcShrink.granges.DAR$distancetoFeature)

binOverFeature(res.lfcShrink.granges.DAR, annotationData = annoDataTxDb,
    radius = 1e+05, nbins = 20, FUN = length, errFun = 0, select = "nearest",
    ylab = "# DARs", xlab = "Distance from TSS", main = "Distribution of DARs around TSS")

## Warning in annotatePeakInBatch(Peaks, AnnotationData = annotationData, output = "nearestLocation", : not all the seqnames of myPeakList is 
##                     in the AnnotationData.

## Warning in annotatePeakInBatch(Peaks, AnnotationData = annotationData, output = "nearestLocation", : Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': JTFH01000247.1, JTFH01000515.1, JTFH01000804.1, JTFH01000876.1, JTFH01001024.1, JTFH01001390.1, JTFH01001405.1, JTFH01001430.1, JTFH01001465.1, JTFH01001478.1, JTFH01001512.1, JTFH01001549.1, JTFH01001680.1, JTFH01001724.1, JTFH01001862.1, JTFH01001929.1, JTFH01001959.1, JTFH01001981.1, JTFH01001998.1, KN707720.1, KN707809.1, KN707828.1, KN707893.1, KN707896.1, JTFH01000028.1, JTFH01000280.1, JTFH01000942.1, JTFH01001023.1, JTFH01001317.1, JTFH01001613.1, JTFH01001899.1, KN707626.1
##   - in 'y': chrM, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270706v1_random, chr1_KI270707v1_random, chr1_KI270708v1_random, chr1_KI270709v1_random, chr1_KI270710v1_random, chr1_KI270711v1_random, chr1_KI270712v1_random, chr1_KI270714v1_random, chr1_KI270759v1_alt, chr1_KI270760v1_alt, chr1_KI270761v1_alt, chr1_KI270762v1_alt, chr1_KI270763v1_alt, chr1_KI270764v1_alt, chr1_KI270765v1_alt, chr1_KI270766v1_alt, chr1_KI270892v1_alt, chr1_KN196472v1_fix, chr1_KN196473v1_fix, chr1_KN196474v1_fix, chr1_KN538360v1_fix, chr1_KN538361v1_fix, chr1_KQ031383v1_fix, chr1_KQ458382v1_alt, chr1_KQ458383v1_alt, chr1_KQ458384v1_alt, chr1_KQ983255v1_alt, chr1_KV880763v1_alt, chr1_KZ208904v1_alt, chr1_KZ208905v1_alt, chr1_KZ208906v1_fix, chr1_KZ559100v1_fix, chr2_GL383521v1_alt, chr2_GL383522v1_alt, chr2_GL582966v2_alt, chr2_KI270715v1_random, chr2_KI270716v1_random, chr2_KI270767v1_alt, chr2_KI270768v1_alt, chr2_KI270769v1_alt, chr2_KI270770v1_alt, chr2_KI270771v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270775v1_alt, chr2_KI270776v1_alt, chr2_KI270893v1_alt, chr2_KI270894v1_alt, chr2_KN538362v1_fix, chr2_KN538363v1_fix, chr2_KQ031384v1_fix, chr2_KQ983256v1_alt, chr2_KZ208907v1_alt, chr2_KZ208908v1_alt, chr2_ML143341v1_fix, chr2_ML143342v1_fix, chr3_GL000221v1_random, chr3_GL383526v1_alt, chr3_JH636055v2_alt, chr3_KI270777v1_alt, chr3_KI270778v1_alt, chr3_KI270779v1_alt, chr3_KI270780v1_alt, chr3_KI270781v1_alt, chr3_KI270782v1_alt, chr3_KI270783v1_alt, chr3_KI270784v1_alt, chr3_KI270895v1_alt, chr3_KI270924v1_alt, chr3_KI270934v1_alt, chr3_KI270935v1_alt, chr3_KI270936v1_alt, chr3_KI270937v1_alt, chr3_KN196475v1_fix, chr3_KN196476v1_fix, chr3_KN538364v1_fix, chr3_KQ031385v1_fix, chr3_KQ031386v1_fix, chr3_KV766192v1_fix, chr3_KZ208909v1_alt, chr3_KZ559101v1_alt, chr3_KZ559102v1_alt, chr3_KZ559103v1_alt, chr3_KZ559104v1_fix, chr3_KZ559105v1_alt, chr3_ML143343v1_alt, chr4_GL000008v2_random, chr4_GL000257v2_alt, chr4_GL383528v1_alt, chr4_KI270785v1_alt, chr4_KI270786v1_alt, chr4_KI270787v1_alt, chr4_KI270788v1_alt, chr4_KI270789v1_alt, chr4_KI270790v1_alt, chr4_KI270896v1_alt, chr4_KI270925v1_alt, chr4_KQ090013v1_alt, chr4_KQ090014v1_alt, chr4_KQ090015v1_alt, chr4_KQ983257v1_fix, chr4_KQ983258v1_alt, chr4_KV766193v1_alt, chr4_ML143344v1_fix, chr4_ML143345v1_fix, chr4_ML143346v1_fix, chr4_ML143347v1_fix, chr4_ML143348v1_fix, chr4_ML143349v1_fix, chr5_GL000208v1_random, chr5_GL383530v1_alt, chr5_GL383531v1_alt, chr5_GL383532v1_alt, chr5_GL949742v1_alt, chr5_KI270791v1_alt, chr5_KI270792v1_alt, chr5_KI270793v1_alt, chr5_KI270794v1_alt, chr5_KI270795v1_alt, chr5_KI270796v1_alt, chr5_KI270897v1_alt, chr5_KI270898v1_alt, chr5_KN196477v1_alt, chr5_KV575243v1_alt, chr5_KV575244v1_fix, chr5_KZ208910v1_alt, chr5_ML143350v1_fix, chr6_GL000250v2_alt, chr6_GL000252v2_alt, chr6_GL000253v2_alt, chr6_GL000254v2_alt, chr6_GL000255v2_alt, chr6_GL000256v2_alt, chr6_GL383533v1_alt, chr6_KB021644v2_alt, chr6_KI270758v1_alt, chr6_KI270797v1_alt, chr6_KI270799v1_alt, chr6_KI270800v1_alt, chr6_KI270801v1_alt, chr6_KI270802v1_alt, chr6_KN196478v1_fix, chr6_KQ031387v1_fix, chr6_KQ090016v1_fix, chr6_KQ090017v1_alt, chr6_KV766194v1_fix, chr6_KZ208911v1_fix, chr6_ML143351v1_fix, chr7_GL383534v2_alt, chr7_KI270805v1_alt, chr7_KI270806v1_alt, chr7_KI270807v1_alt, chr7_KI270808v1_alt, chr7_KI270809v1_alt, chr7_KI270899v1_alt, chr7_KQ031388v1_fix, chr7_KV880764v1_fix, chr7_KV880765v1_fix, chr7_KZ208912v1_fix, chr7_KZ208913v1_alt, chr7_KZ559106v1_alt, chr7_ML143352v1_fix, chr8_KI270810v1_alt, chr8_KI270811v1_alt, chr8_KI270812v1_alt, chr8_KI270814v1_alt, chr8_KI270815v1_alt, chr8_KI270816v1_alt, chr8_KI270817v1_alt, chr8_KI270818v1_alt, chr8_KI270819v1_alt, chr8_KI270820v1_alt, chr8_KI270822v1_alt, chr8_KI270900v1_alt, chr8_KI270901v1_alt, chr8_KI270926v1_alt, chr8_KV880766v1_fix, chr8_KV880767v1_fix, chr8_KZ208914v1_fix, chr8_KZ208915v1_fix, chr8_KZ559107v1_alt, chr9_GL383540v1_alt, chr9_GL383541v1_alt, chr9_GL383542v1_alt, chr9_KI270717v1_random, chr9_KI270718v1_random, chr9_KI270719v1_random, chr9_KI270720v1_random, chr9_KI270823v1_alt, chr9_KN196479v1_fix, chr9_KQ090018v1_alt, chr9_KQ090019v1_alt, chr9_ML143353v1_fix, chr10_GL383545v1_alt, chr10_GL383546v1_alt, chr10_KI270824v1_alt, chr10_KI270825v1_alt, chr10_KN196480v1_fix, chr10_KN538365v1_fix, chr10_KN538366v1_fix, chr10_KN538367v1_fix, chr10_KQ090020v1_alt, chr10_KQ090021v1_fix, chr10_ML143354v1_fix, chr10_ML143355v1_fix, chr11_GL383547v1_alt, chr11_JH159136v1_alt, chr11_JH159137v1_alt, chr11_KI270721v1_random, chr11_KI270826v1_alt, chr11_KI270827v1_alt, chr11_KI270829v1_alt, chr11_KI270831v1_alt, chr11_KI270832v1_alt, chr11_KI270902v1_alt, chr11_KI270903v1_alt, chr11_KI270927v1_alt, chr11_KN196481v1_fix, chr11_KN538368v1_alt, chr11_KQ090022v1_fix, chr11_KQ759759v1_fix, chr11_KV766195v1_fix, chr11_KZ559108v1_fix, chr11_KZ559109v1_fix, chr11_KZ559110v1_alt, chr11_KZ559111v1_alt, chr11_ML143356v1_fix, chr11_ML143357v1_fix, chr11_ML143358v1_fix, chr11_ML143359v1_fix, chr11_ML143360v1_fix, chr12_GL383549v1_alt, chr12_GL383550v2_alt, chr12_GL383551v1_alt, chr12_GL383552v1_alt, chr12_GL877875v1_alt, chr12_GL877876v1_alt, chr12_KI270833v1_alt, chr12_KI270834v1_alt, chr12_KI270835v1_alt, chr12_KI270836v1_alt, chr12_KI270837v1_alt, chr12_KI270904v1_alt, chr12_KN196482v1_fix, chr12_KN538369v1_fix, chr12_KN538370v1_fix, chr12_KQ090023v1_alt, chr12_KQ759760v1_fix, chr12_KZ208916v1_fix, chr12_KZ208917v1_fix, chr12_KZ208918v1_alt, chr12_KZ559112v1_alt, chr12_ML143361v1_fix, chr12_ML143362v1_fix, chr13_KI270838v1_alt, chr13_KI270839v1_alt, chr13_KI270840v1_alt, chr13_KI270841v1_alt, chr13_KI270842v1_alt, chr13_KI270843v1_alt, chr13_KN196483v1_fix, chr13_KN538371v1_fix, chr13_KN538372v1_fix, chr13_KN538373v1_fix, chr13_KQ090024v1_alt, chr13_KQ090025v1_alt, chr13_ML143363v1_fix, chr13_ML143364v1_fix, chr13_ML143365v1_fix, chr13_ML143366v1_fix, chr14_GL000009v2_random, chr14_GL000194v1_random, chr14_KI270722v1_random, chr14_KI270723v1_random, chr14_KI270724v1_random, chr14_KI270725v1_random, chr14_KI270726v1_random, chr14_KI270844v1_alt, chr14_KI270845v1_alt, chr14_KI270846v1_alt, chr14_KI270847v1_alt, chr14_KZ208919v1_alt, chr14_KZ208920v1_fix, chr14_ML143367v1_fix, chr14_ML143368v1_alt, chr15_GL383554v1_alt, chr15_GL383555v2_alt, chr15_KI270727v1_random, chr15_KI270848v1_alt, chr15_KI270849v1_alt, chr15_KI270851v1_alt, chr15_KI270852v1_alt, chr15_KI270906v1_alt, chr15_KN538374v1_fix, chr15_KQ031389v1_alt, chr15_ML143369v1_fix, chr15_ML143370v1_fix, chr15_ML143371v1_fix, chr15_ML143372v1_fix, chr16_GL383556v1_alt, chr16_GL383557v1_alt, chr16_KI270728v1_random, chr16_KI270854v1_alt, chr16_KI270855v1_alt, chr16_KI270856v1_alt, chr16_KQ031390v1_alt, chr16_KQ090026v1_alt, chr16_KQ090027v1_alt, chr16_KV880768v1_fix, chr16_KZ208921v1_alt, chr16_KZ559113v1_fix, chr16_ML143373v1_fix, chr17_GL000258v2_alt, chr17_GL383563v3_alt, chr17_GL383564v2_alt, chr17_GL383565v1_alt, chr17_GL383566v1_alt, chr17_JH159146v1_alt, chr17_JH159147v1_alt, chr17_JH159148v1_alt, chr17_KI270730v1_random, chr17_KI270857v1_alt, chr17_KI270858v1_alt, chr17_KI270859v1_alt, chr17_KI270860v1_alt, chr17_KI270861v1_alt, chr17_KI270862v1_alt, chr17_KI270907v1_alt, chr17_KI270908v1_alt, chr17_KI270909v1_alt, chr17_KI270910v1_alt, chr17_KV575245v1_fix, chr17_KV766196v1_fix, chr17_KV766197v1_alt, chr17_KV766198v1_alt, chr17_KZ559114v1_alt, chr17_ML143374v1_fix, chr17_ML143375v1_fix, chr18_GL383567v1_alt, chr18_GL383568v1_alt, chr18_GL383569v1_alt, chr18_GL383570v1_alt, chr18_GL383571v1_alt, chr18_GL383572v1_alt, chr18_KI270863v1_alt, chr18_KI270864v1_alt, chr18_KI270911v1_alt, chr18_KI270912v1

# add names
res.lfcShrink.granges.annot <- addGeneIDs(res.lfcShrink.granges.annot,
    "org.Hs.eg.db", feature_id_type = "entrez_id", IDs2Add = "symbol")
head(res.lfcShrink.granges.annot, n = 2)

## GRanges object with 2 ranges and 18 metadata columns:
##       seqnames              ranges strand |  baseMean log2FoldChange     lfcSE
##          <Rle>           <IRanges>  <Rle> | <numeric>      <numeric> <numeric>
##    X3     chr1   74673758-74674374      * |   50.2600        3.26583   0.41158
##   X10    chr11 115925001-115925460      * |   27.0066        5.09635   0.82382
##            pvalue        padj        I2        I3        U1        U2        U3
##         <numeric>   <numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
##    X3 9.57734e-17 8.52575e-13  113.3812  105.4563  5.854591   14.2922  12.31558
##   X10 1.52156e-12 4.06347e-09   62.5186   69.8091  0.532236    0.0000   2.17334
##              peak     feature      feature.ranges feature.strand  distance
##       <character> <character>           <IRanges>          <Rle> <integer>
##    X3          X3      127254   74568117-74673792              -         0
##   X10         X10   102724165 115920248-115943181              +         0
##       insideFeature distanceToSite      symbol
##         <character>      <integer> <character>
##    X3  overlapStart              0      ERICH3
##   X10        inside           4752   LINC02703
##   -------
##   seqinfo: 88 sequences from an unspecified genome; no seqlengths

# visualize annotation
pie1(table(res.lfcShrink.granges.annot$insideFeature))

hist(res.lfcShrink.granges.annot$distanceToSite)

binOverFeature(res.lfcShrink.granges.annot, annotationData = annoDataTxDb,
    radius = 1e+05, nbins = 100, FUN = length, errFun = 0, select = "nearest",
    ylab = "# Peaks", xlab = "Distance from TSS", main = "Distribution of peaks around TSS")

## Warning in annotatePeakInBatch(Peaks, AnnotationData = annotationData, output = "nearestLocation", : Found duplicated names in myPeakList. 
##                     Changing the peak names ...

## Warning in annotatePeakInBatch(Peaks, AnnotationData = annotationData, output = "nearestLocation", : not all the seqnames of myPeakList is 
##                     in the AnnotationData.

## Warning in FUN(extractROWS(unlisted_X, IRanges(X_elt_start[i], X_elt_end[i])), : not all the seqnames of myPeakList is 
##                     in the AnnotationData.

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': JTFH01000247.1, JTFH01000515.1, JTFH01000804.1, JTFH01000876.1, JTFH01001024.1, JTFH01001390.1, JTFH01001405.1, JTFH01001430.1, JTFH01001465.1, JTFH01001478.1, JTFH01001512.1, JTFH01001549.1, JTFH01001680.1, JTFH01001724.1, JTFH01001862.1, JTFH01001929.1, JTFH01001959.1, JTFH01001981.1, JTFH01001998.1, KN707720.1, KN707809.1, KN707828.1, KN707893.1, KN707896.1, JTFH01000028.1, JTFH01000280.1, JTFH01000942.1, JTFH01001023.1, JTFH01001317.1, JTFH01001613.1, JTFH01001899.1, KN707626.1
##   - in 'y': chrM, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270706v1_random, chr1_KI270707v1_random, chr1_KI270708v1_random, chr1_KI270709v1_random, chr1_KI270710v1_random, chr1_KI270711v1_random, chr1_KI270712v1_random, chr1_KI270714v1_random, chr1_KI270759v1_alt, chr1_KI270760v1_alt, chr1_KI270761v1_alt, chr1_KI270762v1_alt, chr1_KI270763v1_alt, chr1_KI270764v1_alt, chr1_KI270765v1_alt, chr1_KI270766v1_alt, chr1_KI270892v1_alt, chr1_KN196472v1_fix, chr1_KN196473v1_fix, chr1_KN196474v1_fix, chr1_KN538360v1_fix, chr1_KN538361v1_fix, chr1_KQ031383v1_fix, chr1_KQ458382v1_alt, chr1_KQ458383v1_alt, chr1_KQ458384v1_alt, chr1_KQ983255v1_alt, chr1_KV880763v1_alt, chr1_KZ208904v1_alt, chr1_KZ208905v1_alt, chr1_KZ208906v1_fix, chr1_KZ559100v1_fix, chr2_GL383521v1_alt, chr2_GL383522v1_alt, chr2_GL582966v2_alt, chr2_KI270715v1_random, chr2_KI270716v1_random, chr2_KI270767v1_alt, chr2_KI270768v1_alt, chr2_KI270769v1_alt, chr2_KI270770v1_alt, chr2_KI270771v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270775v1_alt, chr2_KI270776v1_alt, chr2_KI270893v1_alt, chr2_KI270894v1_alt, chr2_KN538362v1_fix, chr2_KN538363v1_fix, chr2_KQ031384v1_fix, chr2_KQ983256v1_alt, chr2_KZ208907v1_alt, chr2_KZ208908v1_alt, chr2_ML143341v1_fix, chr2_ML143342v1_fix, chr3_GL000221v1_random, chr3_GL383526v1_alt, chr3_JH636055v2_alt, chr3_KI270777v1_alt, chr3_KI270778v1_alt, chr3_KI270779v1_alt, chr3_KI270780v1_alt, chr3_KI270781v1_alt, chr3_KI270782v1_alt, chr3_KI270783v1_alt, chr3_KI270784v1_alt, chr3_KI270895v1_alt, chr3_KI270924v1_alt, chr3_KI270934v1_alt, chr3_KI270935v1_alt, chr3_KI270936v1_alt, chr3_KI270937v1_alt, chr3_KN196475v1_fix, chr3_KN196476v1_fix, chr3_KN538364v1_fix, chr3_KQ031385v1_fix, chr3_KQ031386v1_fix, chr3_KV766192v1_fix, chr3_KZ208909v1_alt, chr3_KZ559101v1_alt, chr3_KZ559102v1_alt, chr3_KZ559103v1_alt, chr3_KZ559104v1_fix, chr3_KZ559105v1_alt, chr3_ML143343v1_alt, chr4_GL000008v2_random, chr4_GL000257v2_alt, chr4_GL383528v1_alt, chr4_KI270785v1_alt, chr4_KI270786v1_alt, chr4_KI270787v1_alt, chr4_KI270788v1_alt, chr4_KI270789v1_alt, chr4_KI270790v1_alt, chr4_KI270896v1_alt, chr4_KI270925v1_alt, chr4_KQ090013v1_alt, chr4_KQ090014v1_alt, chr4_KQ090015v1_alt, chr4_KQ983257v1_fix, chr4_KQ983258v1_alt, chr4_KV766193v1_alt, chr4_ML143344v1_fix, chr4_ML143345v1_fix, chr4_ML143346v1_fix, chr4_ML143347v1_fix, chr4_ML143348v1_fix, chr4_ML143349v1_fix, chr5_GL000208v1_random, chr5_GL383530v1_alt, chr5_GL383531v1_alt, chr5_GL383532v1_alt, chr5_GL949742v1_alt, chr5_KI270791v1_alt, chr5_KI270792v1_alt, chr5_KI270793v1_alt, chr5_KI270794v1_alt, chr5_KI270795v1_alt, chr5_KI270796v1_alt, chr5_KI270897v1_alt, chr5_KI270898v1_alt, chr5_KN196477v1_alt, chr5_KV575243v1_alt, chr5_KV575244v1_fix, chr5_KZ208910v1_alt, chr5_ML143350v1_fix, chr6_GL000250v2_alt, chr6_GL000252v2_alt, chr6_GL000253v2_alt, chr6_GL000254v2_alt, chr6_GL000255v2_alt, chr6_GL000256v2_alt, chr6_GL383533v1_alt, chr6_KB021644v2_alt, chr6_KI270758v1_alt, chr6_KI270797v1_alt, chr6_KI270799v1_alt, chr6_KI270800v1_alt, chr6_KI270801v1_alt, chr6_KI270802v1_alt, chr6_KN196478v1_fix, chr6_KQ031387v1_fix, chr6_KQ090016v1_fix, chr6_KQ090017v1_alt, chr6_KV766194v1_fix, chr6_KZ208911v1_fix, chr6_ML143351v1_fix, chr7_GL383534v2_alt, chr7_KI270805v1_alt, chr7_KI270806v1_alt, chr7_KI270807v1_alt, chr7_KI270808v1_alt, chr7_KI270809v1_alt, chr7_KI270899v1_alt, chr7_KQ031388v1_fix, chr7_KV880764v1_fix, chr7_KV880765v1_fix, chr7_KZ208912v1_fix, chr7_KZ208913v1_alt, chr7_KZ559106v1_alt, chr7_ML143352v1_fix, chr8_KI270810v1_alt, chr8_KI270811v1_alt, chr8_KI270812v1_alt, chr8_KI270814v1_alt, chr8_KI270815v1_alt, chr8_KI270816v1_alt, chr8_KI270817v1_alt, chr8_KI270818v1_alt, chr8_KI270819v1_alt, chr8_KI270820v1_alt, chr8_KI270822v1_alt, chr8_KI270900v1_alt, chr8_KI270901v1_alt, chr8_KI270926v1_alt, chr8_KV880766v1_fix, chr8_KV880767v1_fix, chr8_KZ208914v1_fix, chr8_KZ208915v1_fix, chr8_KZ559107v1_alt, chr9_GL383540v1_alt, chr9_GL383541v1_alt, chr9_GL383542v1_alt, chr9_KI270717v1_random, chr9_KI270718v1_random, chr9_KI270719v1_random, chr9_KI270720v1_random, chr9_KI270823v1_alt, chr9_KN196479v1_fix, chr9_KQ090018v1_alt, chr9_KQ090019v1_alt, chr9_ML143353v1_fix, chr10_GL383545v1_alt, chr10_GL383546v1_alt, chr10_KI270824v1_alt, chr10_KI270825v1_alt, chr10_KN196480v1_fix, chr10_KN538365v1_fix, chr10_KN538366v1_fix, chr10_KN538367v1_fix, chr10_KQ090020v1_alt, chr10_KQ090021v1_fix, chr10_ML143354v1_fix, chr10_ML143355v1_fix, chr11_GL383547v1_alt, chr11_JH159136v1_alt, chr11_JH159137v1_alt, chr11_KI270721v1_random, chr11_KI270826v1_alt, chr11_KI270827v1_alt, chr11_KI270829v1_alt, chr11_KI270831v1_alt, chr11_KI270832v1_alt, chr11_KI270902v1_alt, chr11_KI270903v1_alt, chr11_KI270927v1_alt, chr11_KN196481v1_fix, chr11_KN538368v1_alt, chr11_KQ090022v1_fix, chr11_KQ759759v1_fix, chr11_KV766195v1_fix, chr11_KZ559108v1_fix, chr11_KZ559109v1_fix, chr11_KZ559110v1_alt, chr11_KZ559111v1_alt, chr11_ML143356v1_fix, chr11_ML143357v1_fix, chr11_ML143358v1_fix, chr11_ML143359v1_fix, chr11_ML143360v1_fix, chr12_GL383549v1_alt, chr12_GL383550v2_alt, chr12_GL383551v1_alt, chr12_GL383552v1_alt, chr12_GL877875v1_alt, chr12_GL877876v1_alt, chr12_KI270833v1_alt, chr12_KI270834v1_alt, chr12_KI270835v1_alt, chr12_KI270836v1_alt, chr12_KI270837v1_alt, chr12_KI270904v1_alt, chr12_KN196482v1_fix, chr12_KN538369v1_fix, chr12_KN538370v1_fix, chr12_KQ090023v1_alt, chr12_KQ759760v1_fix, chr12_KZ208916v1_fix, chr12_KZ208917v1_fix, chr12_KZ208918v1_alt, chr12_KZ559112v1_alt, chr12_ML143361v1_fix, chr12_ML143362v1_fix, chr13_KI270838v1_alt, chr13_KI270839v1_alt, chr13_KI270840v1_alt, chr13_KI270841v1_alt, chr13_KI270842v1_alt, chr13_KI270843v1_alt, chr13_KN196483v1_fix, chr13_KN538371v1_fix, chr13_KN538372v1_fix, chr13_KN538373v1_fix, chr13_KQ090024v1_alt, chr13_KQ090025v1_alt, chr13_ML143363v1_fix, chr13_ML143364v1_fix, chr13_ML143365v1_fix, chr13_ML143366v1_fix, chr14_GL000009v2_random, chr14_GL000194v1_random, chr14_KI270722v1_random, chr14_KI270723v1_random, chr14_KI270724v1_random, chr14_KI270725v1_random, chr14_KI270726v1_random, chr14_KI270844v1_alt, chr14_KI270845v1_alt, chr14_KI270846v1_alt, chr14_KI270847v1_alt, chr14_KZ208919v1_alt, chr14_KZ208920v1_fix, chr14_ML143367v1_fix, chr14_ML143368v1_alt, chr15_GL383554v1_alt, chr15_GL383555v2_alt, chr15_KI270727v1_random, chr15_KI270848v1_alt, chr15_KI270849v1_alt, chr15_KI270851v1_alt, chr15_KI270852v1_alt, chr15_KI270906v1_alt, chr15_KN538374v1_fix, chr15_KQ031389v1_alt, chr15_ML143369v1_fix, chr15_ML143370v1_fix, chr15_ML143371v1_fix, chr15_ML143372v1_fix, chr16_GL383556v1_alt, chr16_GL383557v1_alt, chr16_KI270728v1_random, chr16_KI270854v1_alt, chr16_KI270855v1_alt, chr16_KI270856v1_alt, chr16_KQ031390v1_alt, chr16_KQ090026v1_alt, chr16_KQ090027v1_alt, chr16_KV880768v1_fix, chr16_KZ208921v1_alt, chr16_KZ559113v1_fix, chr16_ML143373v1_fix, chr17_GL000258v2_alt, chr17_GL383563v3_alt, chr17_GL383564v2_alt, chr17_GL383565v1_alt, chr17_GL383566v1_alt, chr17_JH159146v1_alt, chr17_JH159147v1_alt, chr17_JH159148v1_alt, chr17_KI270730v1_random, chr17_KI270857v1_alt, chr17_KI270858v1_alt, chr17_KI270859v1_alt, chr17_KI270860v1_alt, chr17_KI270861v1_alt, chr17_KI270862v1_alt, chr17_KI270907v1_alt, chr17_KI270908v1_alt, chr17_KI270909v1_alt, chr17_KI270910v1_alt, chr17_KV575245v1_fix, chr17_KV766196v1_fix, chr17_KV766197v1_alt, chr17_KV766198v1_alt, chr17_KZ559114v1_alt, chr17_ML143374v1_fix, chr17_ML143375v1_fix, chr18_GL383567v1_alt, chr18_GL383568v1_alt, chr18_GL383569v1_alt, chr18_GL383570v1_alt, chr18_GL383571v1_alt, chr18_GL383572v1_alt, chr18_KI270863v1_alt, chr18_KI270864v1_alt, chr18_KI270911v1_alt, chr18_KI270912v1

## Warning in FUN(extractROWS(unlisted_X, IRanges(X_elt_start[i], X_elt_end[i])), : not all the seqnames of myPeakList is 
##                     in the AnnotationData.

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': JTFH01000247.1, JTFH01000515.1, JTFH01000804.1, JTFH01000876.1, JTFH01001024.1, JTFH01001390.1, JTFH01001405.1, JTFH01001430.1, JTFH01001465.1, JTFH01001478.1, JTFH01001512.1, JTFH01001549.1, JTFH01001680.1, JTFH01001724.1, JTFH01001862.1, JTFH01001929.1, JTFH01001959.1, JTFH01001981.1, JTFH01001998.1, KN707720.1, KN707809.1, KN707828.1, KN707893.1, KN707896.1, JTFH01000028.1, JTFH01000280.1, JTFH01000942.1, JTFH01001023.1, JTFH01001317.1, JTFH01001613.1, JTFH01001899.1, KN707626.1
##   - in 'y': chrM, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270706v1_random, chr1_KI270707v1_random, chr1_KI270708v1_random, chr1_KI270709v1_random, chr1_KI270710v1_random, chr1_KI270711v1_random, chr1_KI270712v1_random, chr1_KI270714v1_random, chr1_KI270759v1_alt, chr1_KI270760v1_alt, chr1_KI270761v1_alt, chr1_KI270762v1_alt, chr1_KI270763v1_alt, chr1_KI270764v1_alt, chr1_KI270765v1_alt, chr1_KI270766v1_alt, chr1_KI270892v1_alt, chr1_KN196472v1_fix, chr1_KN196473v1_fix, chr1_KN196474v1_fix, chr1_KN538360v1_fix, chr1_KN538361v1_fix, chr1_KQ031383v1_fix, chr1_KQ458382v1_alt, chr1_KQ458383v1_alt, chr1_KQ458384v1_alt, chr1_KQ983255v1_alt, chr1_KV880763v1_alt, chr1_KZ208904v1_alt, chr1_KZ208905v1_alt, chr1_KZ208906v1_fix, chr1_KZ559100v1_fix, chr2_GL383521v1_alt, chr2_GL383522v1_alt, chr2_GL582966v2_alt, chr2_KI270715v1_random, chr2_KI270716v1_random, chr2_KI270767v1_alt, chr2_KI270768v1_alt, chr2_KI270769v1_alt, chr2_KI270770v1_alt, chr2_KI270771v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270775v1_alt, chr2_KI270776v1_alt, chr2_KI270893v1_alt, chr2_KI270894v1_alt, chr2_KN538362v1_fix, chr2_KN538363v1_fix, chr2_KQ031384v1_fix, chr2_KQ983256v1_alt, chr2_KZ208907v1_alt, chr2_KZ208908v1_alt, chr2_ML143341v1_fix, chr2_ML143342v1_fix, chr3_GL000221v1_random, chr3_GL383526v1_alt, chr3_JH636055v2_alt, chr3_KI270777v1_alt, chr3_KI270778v1_alt, chr3_KI270779v1_alt, chr3_KI270780v1_alt, chr3_KI270781v1_alt, chr3_KI270782v1_alt, chr3_KI270783v1_alt, chr3_KI270784v1_alt, chr3_KI270895v1_alt, chr3_KI270924v1_alt, chr3_KI270934v1_alt, chr3_KI270935v1_alt, chr3_KI270936v1_alt, chr3_KI270937v1_alt, chr3_KN196475v1_fix, chr3_KN196476v1_fix, chr3_KN538364v1_fix, chr3_KQ031385v1_fix, chr3_KQ031386v1_fix, chr3_KV766192v1_fix, chr3_KZ208909v1_alt, chr3_KZ559101v1_alt, chr3_KZ559102v1_alt, chr3_KZ559103v1_alt, chr3_KZ559104v1_fix, chr3_KZ559105v1_alt, chr3_ML143343v1_alt, chr4_GL000008v2_random, chr4_GL000257v2_alt, chr4_GL383528v1_alt, chr4_KI270785v1_alt, chr4_KI270786v1_alt, chr4_KI270787v1_alt, chr4_KI270788v1_alt, chr4_KI270789v1_alt, chr4_KI270790v1_alt, chr4_KI270896v1_alt, chr4_KI270925v1_alt, chr4_KQ090013v1_alt, chr4_KQ090014v1_alt, chr4_KQ090015v1_alt, chr4_KQ983257v1_fix, chr4_KQ983258v1_alt, chr4_KV766193v1_alt, chr4_ML143344v1_fix, chr4_ML143345v1_fix, chr4_ML143346v1_fix, chr4_ML143347v1_fix, chr4_ML143348v1_fix, chr4_ML143349v1_fix, chr5_GL000208v1_random, chr5_GL383530v1_alt, chr5_GL383531v1_alt, chr5_GL383532v1_alt, chr5_GL949742v1_alt, chr5_KI270791v1_alt, chr5_KI270792v1_alt, chr5_KI270793v1_alt, chr5_KI270794v1_alt, chr5_KI270795v1_alt, chr5_KI270796v1_alt, chr5_KI270897v1_alt, chr5_KI270898v1_alt, chr5_KN196477v1_alt, chr5_KV575243v1_alt, chr5_KV575244v1_fix, chr5_KZ208910v1_alt, chr5_ML143350v1_fix, chr6_GL000250v2_alt, chr6_GL000252v2_alt, chr6_GL000253v2_alt, chr6_GL000254v2_alt, chr6_GL000255v2_alt, chr6_GL000256v2_alt, chr6_GL383533v1_alt, chr6_KB021644v2_alt, chr6_KI270758v1_alt, chr6_KI270797v1_alt, chr6_KI270799v1_alt, chr6_KI270800v1_alt, chr6_KI270801v1_alt, chr6_KI270802v1_alt, chr6_KN196478v1_fix, chr6_KQ031387v1_fix, chr6_KQ090016v1_fix, chr6_KQ090017v1_alt, chr6_KV766194v1_fix, chr6_KZ208911v1_fix, chr6_ML143351v1_fix, chr7_GL383534v2_alt, chr7_KI270805v1_alt, chr7_KI270806v1_alt, chr7_KI270807v1_alt, chr7_KI270808v1_alt, chr7_KI270809v1_alt, chr7_KI270899v1_alt, chr7_KQ031388v1_fix, chr7_KV880764v1_fix, chr7_KV880765v1_fix, chr7_KZ208912v1_fix, chr7_KZ208913v1_alt, chr7_KZ559106v1_alt, chr7_ML143352v1_fix, chr8_KI270810v1_alt, chr8_KI270811v1_alt, chr8_KI270812v1_alt, chr8_KI270814v1_alt, chr8_KI270815v1_alt, chr8_KI270816v1_alt, chr8_KI270817v1_alt, chr8_KI270818v1_alt, chr8_KI270819v1_alt, chr8_KI270820v1_alt, chr8_KI270822v1_alt, chr8_KI270900v1_alt, chr8_KI270901v1_alt, chr8_KI270926v1_alt, chr8_KV880766v1_fix, chr8_KV880767v1_fix, chr8_KZ208914v1_fix, chr8_KZ208915v1_fix, chr8_KZ559107v1_alt, chr9_GL383540v1_alt, chr9_GL383541v1_alt, chr9_GL383542v1_alt, chr9_KI270717v1_random, chr9_KI270718v1_random, chr9_KI270719v1_random, chr9_KI270720v1_random, chr9_KI270823v1_alt, chr9_KN196479v1_fix, chr9_KQ090018v1_alt, chr9_KQ090019v1_alt, chr9_ML143353v1_fix, chr10_GL383545v1_alt, chr10_GL383546v1_alt, chr10_KI270824v1_alt, chr10_KI270825v1_alt, chr10_KN196480v1_fix, chr10_KN538365v1_fix, chr10_KN538366v1_fix, chr10_KN538367v1_fix, chr10_KQ090020v1_alt, chr10_KQ090021v1_fix, chr10_ML143354v1_fix, chr10_ML143355v1_fix, chr11_GL383547v1_alt, chr11_JH159136v1_alt, chr11_JH159137v1_alt, chr11_KI270721v1_random, chr11_KI270826v1_alt, chr11_KI270827v1_alt, chr11_KI270829v1_alt, chr11_KI270831v1_alt, chr11_KI270832v1_alt, chr11_KI270902v1_alt, chr11_KI270903v1_alt, chr11_KI270927v1_alt, chr11_KN196481v1_fix, chr11_KN538368v1_alt, chr11_KQ090022v1_fix, chr11_KQ759759v1_fix, chr11_KV766195v1_fix, chr11_KZ559108v1_fix, chr11_KZ559109v1_fix, chr11_KZ559110v1_alt, chr11_KZ559111v1_alt, chr11_ML143356v1_fix, chr11_ML143357v1_fix, chr11_ML143358v1_fix, chr11_ML143359v1_fix, chr11_ML143360v1_fix, chr12_GL383549v1_alt, chr12_GL383550v2_alt, chr12_GL383551v1_alt, chr12_GL383552v1_alt, chr12_GL877875v1_alt, chr12_GL877876v1_alt, chr12_KI270833v1_alt, chr12_KI270834v1_alt, chr12_KI270835v1_alt, chr12_KI270836v1_alt, chr12_KI270837v1_alt, chr12_KI270904v1_alt, chr12_KN196482v1_fix, chr12_KN538369v1_fix, chr12_KN538370v1_fix, chr12_KQ090023v1_alt, chr12_KQ759760v1_fix, chr12_KZ208916v1_fix, chr12_KZ208917v1_fix, chr12_KZ208918v1_alt, chr12_KZ559112v1_alt, chr12_ML143361v1_fix, chr12_ML143362v1_fix, chr13_KI270838v1_alt, chr13_KI270839v1_alt, chr13_KI270840v1_alt, chr13_KI270841v1_alt, chr13_KI270842v1_alt, chr13_KI270843v1_alt, chr13_KN196483v1_fix, chr13_KN538371v1_fix, chr13_KN538372v1_fix, chr13_KN538373v1_fix, chr13_KQ090024v1_alt, chr13_KQ090025v1_alt, chr13_ML143363v1_fix, chr13_ML143364v1_fix, chr13_ML143365v1_fix, chr13_ML143366v1_fix, chr14_GL000009v2_random, chr14_GL000194v1_random, chr14_KI270722v1_random, chr14_KI270723v1_random, chr14_KI270724v1_random, chr14_KI270725v1_random, chr14_KI270726v1_random, chr14_KI270844v1_alt, chr14_KI270845v1_alt, chr14_KI270846v1_alt, chr14_KI270847v1_alt, chr14_KZ208919v1_alt, chr14_KZ208920v1_fix, chr14_ML143367v1_fix, chr14_ML143368v1_alt, chr15_GL383554v1_alt, chr15_GL383555v2_alt, chr15_KI270727v1_random, chr15_KI270848v1_alt, chr15_KI270849v1_alt, chr15_KI270851v1_alt, chr15_KI270852v1_alt, chr15_KI270906v1_alt, chr15_KN538374v1_fix, chr15_KQ031389v1_alt, chr15_ML143369v1_fix, chr15_ML143370v1_fix, chr15_ML143371v1_fix, chr15_ML143372v1_fix, chr16_GL383556v1_alt, chr16_GL383557v1_alt, chr16_KI270728v1_random, chr16_KI270854v1_alt, chr16_KI270855v1_alt, chr16_KI270856v1_alt, chr16_KQ031390v1_alt, chr16_KQ090026v1_alt, chr16_KQ090027v1_alt, chr16_KV880768v1_fix, chr16_KZ208921v1_alt, chr16_KZ559113v1_fix, chr16_ML143373v1_fix, chr17_GL000258v2_alt, chr17_GL383563v3_alt, chr17_GL383564v2_alt, chr17_GL383565v1_alt, chr17_GL383566v1_alt, chr17_JH159146v1_alt, chr17_JH159147v1_alt, chr17_JH159148v1_alt, chr17_KI270730v1_random, chr17_KI270857v1_alt, chr17_KI270858v1_alt, chr17_KI270859v1_alt, chr17_KI270860v1_alt, chr17_KI270861v1_alt, chr17_KI270862v1_alt, chr17_KI270907v1_alt, chr17_KI270908v1_alt, chr17_KI270909v1_alt, chr17_KI270910v1_alt, chr17_KV575245v1_fix, chr17_KV766196v1_fix, chr17_KV766197v1_alt, chr17_KV766198v1_alt, chr17_KZ559114v1_alt, chr17_ML143374v1_fix, chr17_ML143375v1_fix, chr18_GL383567v1_alt, chr18_GL383568v1_alt, chr18_GL383569v1_alt, chr18_GL383570v1_alt, chr18_GL383571v1_alt, chr18_GL383572v1_alt, chr18_KI270863v1_alt, chr18_KI270864v1_alt, chr18_KI270911v1_alt, chr18_KI270912v1

## Warning in FUN(extractROWS(unlisted_X, IRanges(X_elt_start[i], X_elt_end[i])), : not all the seqnames of myPeakList is 
##                     in the AnnotationData.

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': JTFH01000247.1, JTFH01000515.1, JTFH01000804.1, JTFH01000876.1, JTFH01001024.1, JTFH01001390.1, JTFH01001405.1, JTFH01001430.1, JTFH01001465.1, JTFH01001478.1, JTFH01001512.1, JTFH01001549.1, JTFH01001680.1, JTFH01001724.1, JTFH01001862.1, JTFH01001929.1, JTFH01001959.1, JTFH01001981.1, JTFH01001998.1, KN707720.1, KN707809.1, KN707828.1, KN707893.1, KN707896.1, JTFH01000028.1, JTFH01000280.1, JTFH01000942.1, JTFH01001023.1, JTFH01001317.1, JTFH01001613.1, JTFH01001899.1, KN707626.1
##   - in 'y': chrM, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270706v1_random, chr1_KI270707v1_random, chr1_KI270708v1_random, chr1_KI270709v1_random, chr1_KI270710v1_random, chr1_KI270711v1_random, chr1_KI270712v1_random, chr1_KI270714v1_random, chr1_KI270759v1_alt, chr1_KI270760v1_alt, chr1_KI270761v1_alt, chr1_KI270762v1_alt, chr1_KI270763v1_alt, chr1_KI270764v1_alt, chr1_KI270765v1_alt, chr1_KI270766v1_alt, chr1_KI270892v1_alt, chr1_KN196472v1_fix, chr1_KN196473v1_fix, chr1_KN196474v1_fix, chr1_KN538360v1_fix, chr1_KN538361v1_fix, chr1_KQ031383v1_fix, chr1_KQ458382v1_alt, chr1_KQ458383v1_alt, chr1_KQ458384v1_alt, chr1_KQ983255v1_alt, chr1_KV880763v1_alt, chr1_KZ208904v1_alt, chr1_KZ208905v1_alt, chr1_KZ208906v1_fix, chr1_KZ559100v1_fix, chr2_GL383521v1_alt, chr2_GL383522v1_alt, chr2_GL582966v2_alt, chr2_KI270715v1_random, chr2_KI270716v1_random, chr2_KI270767v1_alt, chr2_KI270768v1_alt, chr2_KI270769v1_alt, chr2_KI270770v1_alt, chr2_KI270771v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270775v1_alt, chr2_KI270776v1_alt, chr2_KI270893v1_alt, chr2_KI270894v1_alt, chr2_KN538362v1_fix, chr2_KN538363v1_fix, chr2_KQ031384v1_fix, chr2_KQ983256v1_alt, chr2_KZ208907v1_alt, chr2_KZ208908v1_alt, chr2_ML143341v1_fix, chr2_ML143342v1_fix, chr3_GL000221v1_random, chr3_GL383526v1_alt, chr3_JH636055v2_alt, chr3_KI270777v1_alt, chr3_KI270778v1_alt, chr3_KI270779v1_alt, chr3_KI270780v1_alt, chr3_KI270781v1_alt, chr3_KI270782v1_alt, chr3_KI270783v1_alt, chr3_KI270784v1_alt, chr3_KI270895v1_alt, chr3_KI270924v1_alt, chr3_KI270934v1_alt, chr3_KI270935v1_alt, chr3_KI270936v1_alt, chr3_KI270937v1_alt, chr3_KN196475v1_fix, chr3_KN196476v1_fix, chr3_KN538364v1_fix, chr3_KQ031385v1_fix, chr3_KQ031386v1_fix, chr3_KV766192v1_fix, chr3_KZ208909v1_alt, chr3_KZ559101v1_alt, chr3_KZ559102v1_alt, chr3_KZ559103v1_alt, chr3_KZ559104v1_fix, chr3_KZ559105v1_alt, chr3_ML143343v1_alt, chr4_GL000008v2_random, chr4_GL000257v2_alt, chr4_GL383528v1_alt, chr4_KI270785v1_alt, chr4_KI270786v1_alt, chr4_KI270787v1_alt, chr4_KI270788v1_alt, chr4_KI270789v1_alt, chr4_KI270790v1_alt, chr4_KI270896v1_alt, chr4_KI270925v1_alt, chr4_KQ090013v1_alt, chr4_KQ090014v1_alt, chr4_KQ090015v1_alt, chr4_KQ983257v1_fix, chr4_KQ983258v1_alt, chr4_KV766193v1_alt, chr4_ML143344v1_fix, chr4_ML143345v1_fix, chr4_ML143346v1_fix, chr4_ML143347v1_fix, chr4_ML143348v1_fix, chr4_ML143349v1_fix, chr5_GL000208v1_random, chr5_GL383530v1_alt, chr5_GL383531v1_alt, chr5_GL383532v1_alt, chr5_GL949742v1_alt, chr5_KI270791v1_alt, chr5_KI270792v1_alt, chr5_KI270793v1_alt, chr5_KI270794v1_alt, chr5_KI270795v1_alt, chr5_KI270796v1_alt, chr5_KI270897v1_alt, chr5_KI270898v1_alt, chr5_KN196477v1_alt, chr5_KV575243v1_alt, chr5_KV575244v1_fix, chr5_KZ208910v1_alt, chr5_ML143350v1_fix, chr6_GL000250v2_alt, chr6_GL000252v2_alt, chr6_GL000253v2_alt, chr6_GL000254v2_alt, chr6_GL000255v2_alt, chr6_GL000256v2_alt, chr6_GL383533v1_alt, chr6_KB021644v2_alt, chr6_KI270758v1_alt, chr6_KI270797v1_alt, chr6_KI270799v1_alt, chr6_KI270800v1_alt, chr6_KI270801v1_alt, chr6_KI270802v1_alt, chr6_KN196478v1_fix, chr6_KQ031387v1_fix, chr6_KQ090016v1_fix, chr6_KQ090017v1_alt, chr6_KV766194v1_fix, chr6_KZ208911v1_fix, chr6_ML143351v1_fix, chr7_GL383534v2_alt, chr7_KI270805v1_alt, chr7_KI270806v1_alt, chr7_KI270807v1_alt, chr7_KI270808v1_alt, chr7_KI270809v1_alt, chr7_KI270899v1_alt, chr7_KQ031388v1_fix, chr7_KV880764v1_fix, chr7_KV880765v1_fix, chr7_KZ208912v1_fix, chr7_KZ208913v1_alt, chr7_KZ559106v1_alt, chr7_ML143352v1_fix, chr8_KI270810v1_alt, chr8_KI270811v1_alt, chr8_KI270812v1_alt, chr8_KI270814v1_alt, chr8_KI270815v1_alt, chr8_KI270816v1_alt, chr8_KI270817v1_alt, chr8_KI270818v1_alt, chr8_KI270819v1_alt, chr8_KI270820v1_alt, chr8_KI270822v1_alt, chr8_KI270900v1_alt, chr8_KI270901v1_alt, chr8_KI270926v1_alt, chr8_KV880766v1_fix, chr8_KV880767v1_fix, chr8_KZ208914v1_fix, chr8_KZ208915v1_fix, chr8_KZ559107v1_alt, chr9_GL383540v1_alt, chr9_GL383541v1_alt, chr9_GL383542v1_alt, chr9_KI270717v1_random, chr9_KI270718v1_random, chr9_KI270719v1_random, chr9_KI270720v1_random, chr9_KI270823v1_alt, chr9_KN196479v1_fix, chr9_KQ090018v1_alt, chr9_KQ090019v1_alt, chr9_ML143353v1_fix, chr10_GL383545v1_alt, chr10_GL383546v1_alt, chr10_KI270824v1_alt, chr10_KI270825v1_alt, chr10_KN196480v1_fix, chr10_KN538365v1_fix, chr10_KN538366v1_fix, chr10_KN538367v1_fix, chr10_KQ090020v1_alt, chr10_KQ090021v1_fix, chr10_ML143354v1_fix, chr10_ML143355v1_fix, chr11_GL383547v1_alt, chr11_JH159136v1_alt, chr11_JH159137v1_alt, chr11_KI270721v1_random, chr11_KI270826v1_alt, chr11_KI270827v1_alt, chr11_KI270829v1_alt, chr11_KI270831v1_alt, chr11_KI270832v1_alt, chr11_KI270902v1_alt, chr11_KI270903v1_alt, chr11_KI270927v1_alt, chr11_KN196481v1_fix, chr11_KN538368v1_alt, chr11_KQ090022v1_fix, chr11_KQ759759v1_fix, chr11_KV766195v1_fix, chr11_KZ559108v1_fix, chr11_KZ559109v1_fix, chr11_KZ559110v1_alt, chr11_KZ559111v1_alt, chr11_ML143356v1_fix, chr11_ML143357v1_fix, chr11_ML143358v1_fix, chr11_ML143359v1_fix, chr11_ML143360v1_fix, chr12_GL383549v1_alt, chr12_GL383550v2_alt, chr12_GL383551v1_alt, chr12_GL383552v1_alt, chr12_GL877875v1_alt, chr12_GL877876v1_alt, chr12_KI270833v1_alt, chr12_KI270834v1_alt, chr12_KI270835v1_alt, chr12_KI270836v1_alt, chr12_KI270837v1_alt, chr12_KI270904v1_alt, chr12_KN196482v1_fix, chr12_KN538369v1_fix, chr12_KN538370v1_fix, chr12_KQ090023v1_alt, chr12_KQ759760v1_fix, chr12_KZ208916v1_fix, chr12_KZ208917v1_fix, chr12_KZ208918v1_alt, chr12_KZ559112v1_alt, chr12_ML143361v1_fix, chr12_ML143362v1_fix, chr13_KI270838v1_alt, chr13_KI270839v1_alt, chr13_KI270840v1_alt, chr13_KI270841v1_alt, chr13_KI270842v1_alt, chr13_KI270843v1_alt, chr13_KN196483v1_fix, chr13_KN538371v1_fix, chr13_KN538372v1_fix, chr13_KN538373v1_fix, chr13_KQ090024v1_alt, chr13_KQ090025v1_alt, chr13_ML143363v1_fix, chr13_ML143364v1_fix, chr13_ML143365v1_fix, chr13_ML143366v1_fix, chr14_GL000009v2_random, chr14_GL000194v1_random, chr14_KI270722v1_random, chr14_KI270723v1_random, chr14_KI270724v1_random, chr14_KI270725v1_random, chr14_KI270726v1_random, chr14_KI270844v1_alt, chr14_KI270845v1_alt, chr14_KI270846v1_alt, chr14_KI270847v1_alt, chr14_KZ208919v1_alt, chr14_KZ208920v1_fix, chr14_ML143367v1_fix, chr14_ML143368v1_alt, chr15_GL383554v1_alt, chr15_GL383555v2_alt, chr15_KI270727v1_random, chr15_KI270848v1_alt, chr15_KI270849v1_alt, chr15_KI270851v1_alt, chr15_KI270852v1_alt, chr15_KI270906v1_alt, chr15_KN538374v1_fix, chr15_KQ031389v1_alt, chr15_ML143369v1_fix, chr15_ML143370v1_fix, chr15_ML143371v1_fix, chr15_ML143372v1_fix, chr16_GL383556v1_alt, chr16_GL383557v1_alt, chr16_KI270728v1_random, chr16_KI270854v1_alt, chr16_KI270855v1_alt, chr16_KI270856v1_alt, chr16_KQ031390v1_alt, chr16_KQ090026v1_alt, chr16_KQ090027v1_alt, chr16_KV880768v1_fix, chr16_KZ208921v1_alt, chr16_KZ559113v1_fix, chr16_ML143373v1_fix, chr17_GL000258v2_alt, chr17_GL383563v3_alt, chr17_GL383564v2_alt, chr17_GL383565v1_alt, chr17_GL383566v1_alt, chr17_JH159146v1_alt, chr17_JH159147v1_alt, chr17_JH159148v1_alt, chr17_KI270730v1_random, chr17_KI270857v1_alt, chr17_KI270858v1_alt, chr17_KI270859v1_alt, chr17_KI270860v1_alt, chr17_KI270861v1_alt, chr17_KI270862v1_alt, chr17_KI270907v1_alt, chr17_KI270908v1_alt, chr17_KI270909v1_alt, chr17_KI270910v1_alt, chr17_KV575245v1_fix, chr17_KV766196v1_fix, chr17_KV766197v1_alt, chr17_KV766198v1_alt, chr17_KZ559114v1_alt, chr17_ML143374v1_fix, chr17_ML143375v1_fix, chr18_GL383567v1_alt, chr18_GL383568v1_alt, chr18_GL383569v1_alt, chr18_GL383570v1_alt, chr18_GL383571v1_alt, chr18_GL383572v1_alt, chr18_KI270863v1_alt, chr18_KI270864v1_alt, chr18_KI270911v1_alt, chr18_KI270912v1

if (require(TxDb.Hsapiens.UCSC.hg38.knownGene)) {
    aCR <- assignChromosomeRegion(res.lfcShrink.granges.annot,
        nucleotideLevel = FALSE, precedence = c("Promoters",
            "immediateDownstream", "fiveUTRs", "threeUTRs", "Exons",
            "Introns"), TxDb = TxDb.Hsapiens.UCSC.hg38.knownGene)
    barplot(aCR$percentage)
}

## Warning in assignChromosomeRegion(res.lfcShrink.granges.annot, nucleotideLevel =
## FALSE, : peaks.RD has sequence levels not in TxDb.

# remaining significant DA genes
length(res.lfcShrink.granges.annot[res.lfcShrink.granges.annot$padj <
    0.05 & res.lfcShrink.granges.annot$log2FoldChange > 0, ])

## [1] 45

length(res.lfcShrink.granges.annot[res.lfcShrink.granges.annot$padj <
    0.05 & res.lfcShrink.granges.annot$log2FoldChange < 0, ])

## [1] 18

# write output
names(res.lfcShrink.granges.annot) <- NULL
writeOutput(res.lfcShrink.granges.annot, c("Uninfected", "Infected"),
    dir)

Review annotated results in IGV

names(res.lfcShrink.granges.annot) <- NULL
res.lfcShrink.granges.annot.bed <- res.lfcShrink.granges.annot
res.lfcShrink.granges.annot.bed$baseMean <- NULL
res.lfcShrink.granges.annot.bed$peak <- NULL
res.lfcShrink.granges.annot.bed$pvalue <- NULL
res.lfcShrink.granges.annot.bed <- res.lfcShrink.granges.annot.bed[order(res.lfcShrink.granges.annot.bed$padj),
    ]
makebedtable(res.lfcShrink.granges.annot.bed, "res.lfcShrink.granges.annot.html",
    dir)

## [1] "/Volumes/GoogleDrive/My Drive/Greally_Lab/Toxoplasma/Human/ATAC-Seq/Differential Accessibility//res.lfcShrink.granges.annot.html"

MA Plot of annotated results

cutoff <- sort(res.lfcShrink.granges.annot$padj)[20]
df <- as.data.frame(res.lfcShrink.granges.annot) %>%
    mutate(TopGeneLabel = ifelse(padj <= cutoff, symbol, ""))

ggplot(df, aes(x = log2(baseMean), y = log2FoldChange)) + geom_point(aes(colour = padj <
    0.05), shape = 20, size = 0.5) + geom_label_repel(aes(label = TopGeneLabel)) +
    labs(x = "mean of normalised counts", y = "log fold change") +
    ylim(-2, 6) + theme_classic()

## Warning: ggrepel: 2 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

Volcano plot of annotated results

EnhancedVolcano(mcols(res.lfcShrink.granges.annot), lab = mcols(res.lfcShrink.granges.annot)$symbol,
    x = "log2FoldChange", y = "pvalue", xlim = c(-2.5, 6), pCutoff = 0.05,
    pCutoffCol = "padj", FCcutoff = 2, drawConnectors = TRUE,
    title = "", subtitle = "", gridlines.minor = FALSE, gridlines.major = FALSE,
    col = c("black", "black", "black", "red3"))

Heatmap of annotated peaks

# set up matrix
dds_vst.mat <- as.matrix(mcols(res.lfcShrink.granges.annot[,c("I2", "I3", "U1", "U2", "U3")]))
rownames(dds_vst.mat) <- res.lfcShrink.granges.annot$symbol
dds_vst.mat <- dds_vst.mat[,c(3,4,5,1,2)]
# getting differentially expressed genes 
dds_vst.mat.DE <- dds_vst.mat[which(mcols(res.lfcShrink.granges.annot)$padj < 0.05),]

colors <- viridis(5)[c(1,5)]
col <- list(Condition = c(
            "Uninfected" = colors[1],
            "Infected" = colors[2]))

condition <- factor(c(rep("Uninfected", 3), rep("Infected", 2)), levels = c("Uninfected", "Infected"))
ha <- HeatmapAnnotation(Condition = condition, col = col)

scaled.mat <- t(scale(t(dds_vst.mat.DE),center=TRUE,scale=TRUE))

Heatmap(scaled.mat,
        name = "Z-score", #title of legend
        #col=magma(100),
        row_names_gp = gpar(fontsize = 7), # Text size for row names
        top_annotation = ha,
        border = TRUE,
        cluster_rows = TRUE,
        cluster_columns = FALSE,
        show_row_names = TRUE,
        column_names_rot = 0,
        show_parent_dend_line = FALSE,
        row_dend_width = unit(20, "mm"))

Plot accessibility changes over chromosomes

res.lfcShrink.granges.plot <- res.lfcShrink.granges.annot
mcols(res.lfcShrink.granges.plot)$score <- -log10(res.lfcShrink.granges.plot$padj)
res.lfcShrink.granges.plot <- keepSeqlevels(res.lfcShrink.granges.plot,
    pruning.mode = "tidy", c(paste0("chr", 1:21), "chrX", "chrY"))
label <- res.lfcShrink.granges.plot[res.lfcShrink.granges.plot$padj <
    0.05]

plotGrandLinear(res.lfcShrink.granges.plot, aes(y = score), color = turbo(2),
    cutoff = -log10(0.05), cutoff.color = "black", cutoff.size = 1,
    ylab = "-log10(padj)", spaceline = TRUE, highlight.label.size = 3,
    highlight.gr = label, highlight.name = "symbol") + theme(axis.text.x = element_text(angle = 45,
    hjust = 1))

## using coord:genome to parse x scale

autoplot(res.lfcShrink.granges.plot[res.lfcShrink.granges.plot$padj <
    0.05, ], layout = "karyogram", aes(color = log2FoldChange,
    fill = log2FoldChange)) + scale_fill_viridis_c(option = "magma") +
    scale_color_viridis_c(option = "magma")

## Warning in getIdeoGR(data): geom(ideogram) need valid seqlengths information for accurate mapping,
##                  now use reduced information as ideogram...

## Warning in getIdeoGR(data): geom(ideogram) need valid seqlengths information for accurate mapping,
##                  now use reduced information as ideogram...

## Scale for 'x' is already present. Adding another scale for 'x', which will
## replace the existing scale.

## Scale for 'x' is already present. Adding another scale for 'x', which will
## replace the existing scale.

Volcano plot of all peaks with annotated peaks labeled

# merge
res.lfcShrink.granges.merge <- rbind.fill(as.data.frame(mcols(res.lfcShrink.granges)), as.data.frame(mcols(res.lfcShrink.granges.annot)))

keyvals <- ifelse(
    res.lfcShrink.granges.merge$log2FoldChange < -2, colors[1],
    ifelse(res.lfcShrink.granges.merge$log2FoldChange > 2, colors[2],
    'black'))
keyvals[is.na(keyvals)] <- 'black'
  
EnhancedVolcano(res.lfcShrink.granges.merge,
  lab = res.lfcShrink.granges.merge$symbol,
  x = 'log2FoldChange',
  y = 'pvalue',
  pCutoffCol = 'padj',
  pCutoff = 0.05,
  FCcutoff = 2,
  gridlines.major = FALSE,
  gridlines.minor = FALSE,
  pointSize = 3.0,
  labSize = 4.0,
  labCol = 'black',
  labFace = 'bold',
  boxedLabels = FALSE,
  colAlpha = 4/5,
  drawConnectors = TRUE,
  widthConnectors = 1.0,
  colConnectors = 'black',
  legendPosition= 'none',
  subtitle = NULL,
  #colCustom = keyvals,
  col=c('black', 'black', 'black', colors[2]),
  title = NULL,
  caption = NULL)